Adamw

You have a very noisy TPS (most evo's do), if you ecu log it at higher frequency you will find there will be regular short TPS delta spikes above 5.  I have the TPS delta lockout set to 15 in my evo 7.   

Your CLL status says it was locked out due to MAP delta at the time you last saved the map.  This only gives a single snapshot however so may not be your only issue.  The Closed loop lambda 1 status runtime should normally tell you what is going on.  

Its certainly a pretty odd setup he has done there with equation load source set to BAP, then an alpha N fuel map overlayed with a speed density map...  Im not sure if he has out-smarted himself or has ended up with the odd mess when trying to solve a problem.  There are some other issues in there such as the IAT trim is still enabled in modelled mode and the charge temp approximation table has zero coolant bias so you will be getting twice as much air temp correction than you should be.  
Typically for your application just a single fuel table withh TPS as the load axis will do it, equation load source may need to be MAP if any of the bullet points below apply, otherwise load source = BAP will usually work better for NA ITB with high overlap.  
equation load source = MAP if any of the following are true:
The engine has an idle valve The vehicle has vacuum assisted brakes connected to manifold vacuum. The engine is boosted. There is a restrictive airbox/filter arrangement. If you arent in a big hurry, Im in AKL and could take care of it one weekend.  Im pretty much booked solid for about the next 6 weeks though.  

Its certainly a pretty odd setup he has done there with equation load source set to BAP, then an alpha N fuel map overlayed with a speed density map...  Im not sure if he has out-smarted himself or has ended up with the odd mess when trying to solve a problem.  There are some other issues in there such as the IAT trim is still enabled in modelled mode and the charge temp approximation table has zero coolant bias so you will be getting twice as much air temp correction than you should be.  
Typically for your application just a single fuel table withh TPS as the load axis will do it, equation load source may need to be MAP if any of the bullet points below apply, otherwise load source = BAP will usually work better for NA ITB with high overlap.  
equation load source = MAP if any of the following are true:
The engine has an idle valve The vehicle has vacuum assisted brakes connected to manifold vacuum. The engine is boosted. There is a restrictive airbox/filter arrangement. If you arent in a big hurry, Im in AKL and could take care of it one weekend.  Im pretty much booked solid for about the next 6 weeks though.  

Hmm, it looks like there might be a broken link somewhere.  
You can manually navigate to it in Help > contents tab > G4X and G5 ECU Tuning Functions > Electronic Throttle Control > E-Throttle First Time Setup

Ok, the firmware engineer says the trig 1 state suggests it is small spikes of ignition noise getting into the trigger signal and when these are big enough they will be interpreted as extra "teeth".  You have two variations of errors in your scopes, one caused by noise on trig 2 and one caused by noise on trig 1 - so the noise source is likely coming from something that is common to both.  These spikes arent always big enough/long enough to be captured in the scope but there are a couple of the more obvious ones shown below and you can see the trigger 1 state resets to idle(0) when these occur.
  
 
So, a couple of things to look at:
Rotor phasing - wind the engine to about 20deg BTDC by hand, pull the distributor cap off and check the rotor is roughly centred under a post in the cap.  Sometimes to make it easier to tell, before pulling off the cap you can mark the OD of the distributor with a felt pen where the post sits, then remove the cap and check the rotor is pointing at that mark.  If you dont have a 20BTDC mark just guestimate based on the 10deg mark will be close enough. Ignitor ground.  The 4AGE ignitor grounds through its body - which is then hanging on a bracket on the coil etc so there is a lot of potential for a poor ground connection.  Remove the coil and ignitor, bracket etc, make sure all contact points between the ignitor, bracket and chassis are clean, no paint where it mounts to the body etc.    There should be noise filter on the coil power supply somewhere, I dont know where it is physically located but it should be close to the coil, check it is present.  

Can you do a log with the "PID setup" set to traction control, I think the oscillation is possibly the torque recovery rate is too high (bringing torque back in too quickly when slip drops) or the proportional is too high (taking too much torque out too quickly)

For ECU hold power to work the wiring will need to be as per factory.  The main points:
An ignition switch signal that is +12V when ignition is on, to Pin 85. The main relay coil connected to pin 59, the other side of the relay coil connected to ground. +12V Power supply from the main relay high current contacts to pins 99 & 100.  The supply to that relay must be constant 12V - not supplied from some other relay. +12V battery feed (constant 12V) to pin 93. And of course at least some of the main grounds connected.

You cant connect the lambda to the factory bus, you are crashing the bus so nothing will work.  CAN 2 needs to be set to 350Z mode and only CAN 1 can have aftermarket devices connected.  

One of them will be used for both sync (trigger) and vvt, the other just VVT only.  Connect the left-hand cam sensor to trigger 2 as mentioned earlier.

Not really, the master fuel is a multiplier so will affect the size of the final numbers in the fuel table, the max value that the fuel table can take is 150, so if you for example had the master set too small you might start tuning at low rpm/load, and have values of say 100 in the fuel table, then when you get to higher loads you find your fuel table number is maxed out so you cant add any more fuel.  Conversely, if your master was set too big, then you could have very small numbers in the fuel table, which would affect the resolution of adjustment you have.  
If the values in the middle of the fuel table are around say 30-90, then the master is fine.

If you pull the sensor out of the block but leave it plugged in, then do a trigger scope with the sensor just hanging in free air (dont crank engine) you should see 3.5-5V showing on the trigger 1 trace.  Then if you put something iron based in front of the sensor and do another scope capture you should then see near 0V.  These tests will at least confirm the sensor is working and is wired correctly.  

The cam position would be able to go to "-10" instead of stopping at zero, the ecu will report errors and disable cam control if it goes more than a couple of degrees below zero.  

The wrx sensors look identical to that.  They are pinned:
5V Gnd TP Sub 5V Gnd TP Mian.   Im pretty sure the pin numbers are printed on the back of the plug near the wires.  

This is how normalised mode works. 
With normalised mode the ecu is comparing the noise level of the current combustion event to the previous few "learnt" combustion events.  If you are operating under reasonably stable conditions then suddenly increase load or RPM, then the first few combustion events at that new higher load will now be generating more noise than the previous events it is comparing to.  So to account for this, when there is a sudden change in load or RPM (this is determined by the RPM/MAP/TPS delta level settings, then the threshold is increased by the "Threshold gain" for the number of cycles set in "Delta hold".   
With normalised mode you would usually have a "flat" threshold table, and the threshold should only need to step up for a short time when there is a significant change in load or RPM.  You should not need to increase threshold with RPM or boost like your threshold table is, this suggests something is not right in the setup or possibly mechanical.  I notice you have a 2.5L whereas our car was a 2.0 so possibly the knock frequency is not ideal.  You could try it at 6,7 and say 13Khz to see if the noise levels look less erratic.  Your ignition advance is quite low so I doubt there is knock, but it is a little odd that your cyl 4 knock level is mostly the one that is erratic.  
A quirk I found in our subaru was the sharp click from the AC clutch turning on/off in auto mode would cause a spike in knock level, I got around this by disabling knock for a few tenths of a second before the clutch switched on of off.  I see that has caused 1 spike in your log but it is not your main issue, just something to keep in mind if you start seeing random spikes or retard.  

For the trigger scope capture you need to go to >ECU controls>Trigger Scope, then hit the capture button, once the screen has a waveform showing on the screen then click save.  Do one at idle and one with a free rev to about 5000.  

No, it should be the opposite, increasing the master increases the injector PW.  Set it to 5 to see if it improves the stumble or response issue, we dont care if the idle AFR is richer as that is not where your issue is. 
 
The master fuel setting is the overall fuel scaler.  The Fuel flow table is irrelevant, this is only used for fuel consumption calculation.   Adjust the master fuel until the engine runs then tune the individual cells in the fuel table to achieve the target AFR under all operating conditions.

You are really going to need the lambda working to be able to tune it, but my guess would be you dont have enough fuel, try increasing or decreasing master fuel to see if it improves in either direction.  

I was in the middle of a reply when Vaughan beat me to it.  So here is mine anyhow:
Are you capable of basic wiring/crimping yourself?  Link do offer a variety of CAN cables that could be used, but in this case since neither the keypad or CAN lambda has a built-in termination resistor I think it would be nicer to build your own bus.
Schematically we want to achieve something like this:

 
In practice there are several different ways to achieve this. One option is to arrange like a daisy chain, provided it does not need to be waterproof you can often crimp two wires into a single connector pin so a splice is not needed.  Something like this (not shown but CAN H & L would be twisted):

 
Using Link accessories would end up something like below, so possibly more complicated and expensive than it needs to be:

Your MAP sensor isnt working in the log so it has about 300% more fuel dumping in than it normally would, so start by fixing that to see if it helps.  You can test the ignition outputs by pulling the spark plugs out so you can see them, then use the ignition test function to test spark each output.  

If you have a plug-in ecu the hardware is already built-in and the hold power is already set up and working in the base map, you dont need to do anything.

From memory the gain and update rate table examples given by me above are from my Evo road car (pretty much dead stock evo 7) the lambda probe is very close to the turbine outlet probably at the most 500mm from the exhaust port, in this car I have the reactivation delay set to 3 samples.  In our WRX11 test car which also has the probe right after the turbine - but has much longer manifold primaries etc (probably more like 1500mm from port to probe) I have reactivation delay set to 5 samples.  The update rate table is similar in both cars, the subaru could actually do with less than 1Hz at idle as it takes about 3 secs to respond to a change of PW but 1Hz is currently the lowest it can do. 
So what this means is in my evo with the reactivation delay set to 3 samples, if CLL was temporarily disabled due to over-run fuel cut or similar around idle where my update rate is 1Hz (1 sample per second), then CLL would be re-enabled 3 secs later.  To give an example at the other end of the table, if I hit the RPM limit at 7000RPM where my update rate was 10Hz, then CLL would be disabled for only 0.3s.    

You can just put zeros in your 3D trim limit tables where you dont want CLL to operate.  
Not possible as the LTFT table uses a GP table which has a max cell count of 16 x 11, whereas the main fuel table cell count is 22 x 20.  If your Fuel table is 16 x 11 or less then you can use the import/export tool to copy it to the LTFT to get the same axes.

The most important one I see in the list that may affect you is to check the base timing after updating.  There was a change in 6.20 that moved the trigger offset by 1 tooth with the trigger some missing tooth trigger modes.  

Assuming the ecu has already been unlocked, then also check the antitheft runtime, the ecu will cut fuel and spark if the antitheft conditions are not satisfied.