Adamw

With the old MXL dashes they have a fixed, pre-configured CAN template so make sure it has all the channels you want (basically only a small selection of what is in the generic dash stream).  I will see if I can get a pic.  Also the old RS2 logging software was fairly capable, but wasnt particularly nice to use for data analysis.
You will only be able to display and log the below list from the ecu, + I think the pro has 8 analog inputs, 4 digital that could be used in the dash (not sent back to ecu):

 

For the non VVT engine, assuming it has a proper 60-2 pattern and not the original weird Renault 60-1-1, then you can connect a MAP sensor to one intake port and use the MAP level sync function to get full sequential and direct spark.
For the VVT engine you will need a cam sensor (on a part of the cam, not the sprocket).  Clio 3 flywheel and cam would be the easiest if that is possible.  Otherwise if it again has a proper 60-2 pattern and not the weird Renault 60-1-1 then you are pretty free what you can do on the cam.  It will need 2 teeth or more and some non-symmetrical pattern that is different on one crank rev compared to the other so the ecu can determine phase.  So you could do something like toyota - 3 evenly spaced teeth all the same size, or in a 4-1 pattern, or the common "2 long, 2 short" like the clio 3 had.  

Yep, crank sensor is wired back to front.

Can you load the attached ecu log set and do a similar test then download the ecu log.  The PC log is a bit slow to see enough detail but it appears to show the pedal (APS) only reducing at about the same time as the spike in RPM.  This maybe something to do with the weird cable set up that the altezzas have.  

Ethrottle test.llsx

I notice you have really large VE numbers at idle and I have seen this before with a couple of other users with ID1050X injectors.  So Im suspicious that the ID supplied deadtimes may be a bit off when using Link drivers (they use Motec M1's for their characterisation). So you will probably find more error at idle and it will work better at higher loads.
A couple of things I noticed in your tune which changing will probably help this error a tiny bit:
Your deadtime table has fuel pressure on the Y axis, it should instead be differential fuel pressure (Pressure across the injector is what affects deadtimes). I think the Stoich ratio for E30 should be more like 13.0, that is assuming Eth is 9.0 and petrol is 14.7 and we are using a 30/70 split between those. I would experiment with increasing the deadtimes a little to see if you can get this open loop target correction working better and more realistic VE numbers around idle.  I would typically expect VE of 50-65% at idle, you have 78ish.   
 
 

The factory sensor is connected to the ecu dedicated knock input pin, you dont need to change any wiring or add any sensors.  

Yeah not much info on that one.  From the few bits of vague info I fairly confident of these ones:
7Pin:
A = sensor ground. 
B = +12V supply to CAS.
D = Ignitor ground (ground to engine)
E = Ign signal from ECU.
 
I assume C is one of the triggers and possibly F or G (I think G is possibly labeled wrong on your drawing).  So I would connect up just A & B, turn the dizzy by hand while holding a multimeter on C,F & G to see which have a pulsing signal coming out.
One the 3pin connector I think it would only need 12V on A (coil supply).  
 
 
 

Yeah, probably wont work well if you are doing PWM due to small timing differences but normal on/off will be ok.  

Ok that should be fine.  I would expect those coils to be happy up with up to about 500mv offset.
So if it runs ok with B grounded to the cyl head then I would just leave it like that, it will be difficult to find why it is not happy with ECU ground without a scope etc.  I have seen many of those coils grounded that way working without drama although I do prefer to have that referencing ecu ground.      

Assuming MAP and charge temp are reading correct, if the air per cyl estimate is smaller than you expect it should be then that generally means the engine is receiving more fuel mass than the ecu believes it is injecting based on the metrics it has been given to calculate fuel mass. - so the net effect is to get the air/fuel ratio correct you have had to tell the engine there is less air going in (ie you have smaller VE numbers in the fuel table than realistic).   
There are many possibilities where that error is coming from, fuel density settings, stoich ratio setting, injector flow rate or dead times, fuel pressure etc. If the air mass estimated is reading half what you expect it suggests there is a fairly significant error coming from somewhere.   
It would generally not cause too much of a tuning issue but some of the fuel model possibly wont work as well as it should if the estimates are a long way off.   
If you attach a copy of the tune and short PC log I will take a look.  

Note the ECU only outputs a ground signal that goes to the fuel pump relay, it does not supply power to anything.  It sounds like you are expecting something different?
I have stitched together a few pages from the factory wiring diagram to show how the stock FP circuit works in the pic below (click on it for a bigger version). 
12V comes from the battery at top right to FPump relay 1, this relay turns on with the ign switch - it is not controlled by the ecu.  When ign is on 12V will come out of FP relay 1, pin 1 and supplies 12V to pin 4 on FPump relay 2, when the ECU grounds the Ign 3 pin this relay closes and the fuel pump will run.  FPump relay 3 just controls whether the power from relay 2 goes straight to the fuel pump for high speed mode (green route) or through the fuel pump resistor for low speed mode (purple route).   

 

Ok, finally had a chance to implement your suggestions, and after some trial and error, it works!
Turns out the MXG is in fact quick enough to send the RPM and EMAP data to the Can Lambdas to keep them from turning on when the key is at the ON position. It is sending the RPM and EMAP data to the Can Lambdas, and they are all staying disabled while the engine is off. Thanks to this, I still have a few streams for sending data over to the MXG. 
 

I had to send the dash back to AIM. It was a quick fix but something only they could do. 
It's working again now. Problem solved. 

Yes the ecu can control the honda valve no worries, this is what we call a "3 wire" valve.  12V to the center pin, the two outer pins need to be connected to either Aux 1 & 2 or Aux 3 & 4.
I dont have any personal experience with it to say if it can flow enough air for your particular engine or not but I would expect so based on the size of the ports.  You wont need the water side connected.  
Note for your 2 wire ignition coils, these will need ignitors/coil drivers to drive them, they can be connected directly to the ecu.  

The charge temp table from our WRX11 base map will be pretty close.  The general way to tune the charge temp table is to hold one variable as constant as possible while varying the other one.  On our subaru it was easy with the top mount intercooler, with my intercooler fan off I could just hold it at constant load/speed on the dyno, the water temp would stay reasonably static while the IAT would quickly run away.  If charge temp approximation number is correct the lambda will stay on target.  If it goes lean as IAT increases then you need more bias towards coolant.  I do that at say 6 different loads/RPM's and that gives you a pretty good feel for the trend.
IAT fuel trim should be off.  

You can import the fuel table from our G4X WRX11 base map which is an EJ205 using modelled fuel.  It will probably be a decent starting point.  

Yeah you have caught it in one of those scopes.  If you look at the parameter "trigger 1 state" it should change from "counting" to "tooth after sync" once its counted 12T and is expecting to see the sync again.  Provided it sees the sync again where it is expected to be then it will go back to counting and do the same 12T later.  
In the places where they trigger errors occur however we see the state change to "tooth after sync" after only 10 or 11 teeth, not 12.  So this means the ecu must have received a random "spike" on the trigger 1 signal that has met all the criteria to be accepted as a "tooth".  The trigger scope is too low res and the sample rate is too low to show this spike.  
Do you know anyone with a standalone oscilloscope?  What does it have for an ignition system?  Do you have resistor spark plugs?  If you go to >help>ecu information, what maincode firmware version do you have?

Both can work very well and can acheive smooth and fast arrest of wheel slip. 
The G4+ was a lot more basic, it could only apply retard and cut proportionally with each other at the same time for torque reduction.  G4X torque reduction is more sophisticated with a dedicated torque management function.  So the ecu can estimate how much torque the engine is making and achieve the required reduction using a mixture of retard, cuts, e-throttle & closed loop boost control.  It will initially use retard, then cut to arrest slip since these have immediate effect on torque, but also initiate reduction of throttle and boost at the same time, when these slower moving torque reduction methods catch up the cuts and retard will be removed or reduced.  This allows less reliance on cuts and retard which can be quite hard on the engine especially in cases such as a wet endurance race where your TC may be working hard for hours. 
G4+ only had 2 slip tables, G4X has 2 slip tables and an overlay table, and you can also add a GP PWM to one axis of one of the tables if you want to add further control dimensions.  
G4X has further improvements to the slip sources also - for example it can be set up to use the "outside wheel" (uses the on board acclerometers to determine which way the car is cornering) for the driving wheel speed source which works better for some types of diffs.  It can also switch between two different wheel speed calibrations if for example you have different sized wet and dry tyres or drag/road tyres etc.
 

Both can work very well and can acheive smooth and fast arrest of wheel slip. 
The G4+ was a lot more basic, it could only apply retard and cut proportionally with each other at the same time for torque reduction.  G4X torque reduction is more sophisticated with a dedicated torque management function.  So the ecu can estimate how much torque the engine is making and achieve the required reduction using a mixture of retard, cuts, e-throttle & closed loop boost control.  It will initially use retard, then cut to arrest slip since these have immediate effect on torque, but also initiate reduction of throttle and boost at the same time, when these slower moving torque reduction methods catch up the cuts and retard will be removed or reduced.  This allows less reliance on cuts and retard which can be quite hard on the engine especially in cases such as a wet endurance race where your TC may be working hard for hours. 
G4+ only had 2 slip tables, G4X has 2 slip tables and an overlay table, and you can also add a GP PWM to one axis of one of the tables if you want to add further control dimensions.  
G4X has further improvements to the slip sources also - for example it can be set up to use the "outside wheel" (uses the on board acclerometers to determine which way the car is cornering) for the driving wheel speed source which works better for some types of diffs.  It can also switch between two different wheel speed calibrations if for example you have different sized wet and dry tyres or drag/road tyres etc.
 

I wouldnt say perfectly normal, but certainly not uncommon and I see a lot worse daily.  It can take a lot of time to get the various compensations dailed in to cover all operating conditions and most dont care - as long as its safe and not misfiring...
 
    Not at all.

Use 1JZ vvti trigger mode, offset should be close to zero with that but you need to confirm with a timing light.  
Since you have an idle valve, you will need Equation load source set to MAP and the MAP sensor connected to the same manifold so that the ecu can compensate for the varying air volume passing through the idle valve.  
Turn off CLL until fuel table is tuned.
Turn on Async injection with min async PW = 1.0ms.  And put something like 5 in your accel sens table.  
Assuming it is NA, change your lambda target table so that 0.87 is the smallest value in there (WOT).  I normally have around 095 at idle, 0.9 at 40% TP and 0.87 at WOT. 
For your ign table copy your 60%TP row down to the 100% row, even then it will be on the conservative side.
Also, not related to your running problem, but I would suggest taking a whole lot of rows out of your fuel and ign tables, you are only creating a lot of tuning work by having so many.  For ITB's I usually do TP 0%,2,5,8,11,15,20,30,40,60,100.  Only add extra cells if there is found to be some area that is not taken care of by linear interpolation during tuning.  

Example below would give you boost table one with switch in pos 1, boost table 2 when switch is in pos 2 or 3, and boost table 3 when switch is in pos 4 or higher.  

Example below would switch to boost table 2 for any switch position above 2.

Yes, it would be basically the same as my first example above.

Your gauge doesnt have CAN bus.  You will need something newer that has CAN.  If you want a gauge at the same time then the X-series would probably be the most cost effective option.