Adamw

I will add a little more info here since I have quite a bit of experience in this strategy.
I agree with ECU settings as per Scott's suggestions, but I would say nearly always it would be worth while to have a "MAP sensor" connected also.  In this case however you don't connect the MAP sensor to manifold, you connect it to the airbox (your FPR reference should also be tee'd to this same measurement point).  The ecu and FPR will then keep fuelling more consistent when the airbox is subjected to aerodynamic effects.  If airbox and general intake design is good I often see 4-10Kpa positive pressure (ie you will need 4-10% more fuel) on high speed sections so it can be a significant effect.

Can you attach your .pclr also?

Yes it is a reference to TDC, but it doesn't need to occur at TDC. 
You set your trigger offset in the software (calibrate trigger menu).  This is the angular distance the crank must rotate from the first tooth after the gap to TDC.  However you don't need to measure anything, just take a guess then crank it with a timing light on and adjust until the marks line up.  More info in the help file and it will make more sense when you actually do it.
I think you will find the vast majority of OEM triggers that use missing tooth wheels, the gap is never at TDC.  Ford's favourite for instance is usually 90ATDC. There are many reasons, one I already mentioned is the crank acceleration near TDC, another is if your missing tooth is in an area where your ignition event must occur (say 0-45°BTDC) there is the possibility that it would be less accurately positioned since there is no tooth to reference.  

I just noticed you have some really odd idle ignition control table.  50deg retard all over?  So turn off idle ignition control for now.  After that, start engine and adjust your master fuel up or down (pg up & pg down keys is easiest) until your AFR is in the ball park.

Tony,
An engine like this will need significant valve timing overlap so a MAP based load will not work well even with a single throttle body.  NA race engines is mostly all I do (normally ITB though) so I know this application well.  I normally still have a MAP sensor connected but only plumbed to the airbox to allow for aero effects at highspeed.  I would normally have the  FPR reference tee'd to the same location.  Load axis for both fuel & ign maps should be TPS.  You say "I only care about full throttle", but remember the engine must still accelerate out of low speed corners and must drive in pits and idle at dummy grid etc.
Another observation; your MAP on the graph above shows a significant trend downwards with increasing RPM.  To me that suggests your intake is very restrictive and is already loosing you power at just 6000RPM.  You will need to rethink that if you intend to make power at 10000...

The setting you are looking for is found under Engine Protection>MAP Limit Table 1.  It will most likely look something like below. Try increasing the MAP values that I have highlighted by about 10%.

Further to Jonny's comment, you can easily verify your wiring using the injector test function.  With ECU connected to laptop and ignition turned on, fuel pump turned off, Go to Fuel>Fuel Setup>Injector test. Set it to Inj 1 (2ms 10Hz), you should hear No 1 injector clicking.

I have never personally done it with a vipec but you can upgrade a G4 tune file to a G4+ so I assume the same will work for i88.
The secret is you need to be connected to a live/powered up ECU, before the software will allow you to open an old format map.
So, with Laptop connected to ECU & ignition/power on, open new G4+ software.  Then go to file>open and browse for your old V88 tune file, it should open up and convert to i88 file, you can then save it with a new name.

On a stock road going evo there are no spare digital inputs left on the ECU connector so you have to use the Expansion connector.  However since yours is a "race car" I guess you no longer have air conditioning fitted?  If that assumption is correct then you could connect your Antilag enable switch to one of the DI's that used to be associated with A/C.  ECU pinout is in the help file, you can possibly use DI1 on pin 45 or DI5 on pin 11.

With engine running, and laptop connected, go to ecu settings>triggers>calibrate, then click on "set base timing".  This will bring up a new screen where you can set whatever figure you want to lock the timing to.  For you probably 10° is a convenient number.  The with timing light pointing at pulley, then adjust the "offset" number up or down until the 10° mark on your pulley/engine lines up.
After you click done on that screen you need to hit F4 to save changes to ECU.

Vincent,
Trying to get some effect by adjusting the main fuel & Ign maps as you have proposed will not achieve much.  With proper setup "two step" or launch control you should be well into positive pressure and not down in the vacuum region that you have highlighted.
Since you are 4WD you will probably want to use Mode 2 - this is commonly known as "two step".  It is a fixed RPM limiter usually combined with extra fuel and very retarded ign.  For this mode you would normally activate it with a switch on the clutch pedal as it must be turned off as soon as you start moving.
Settings for this aren't easy to guess and are usually done by trial and error.  Unless someone here has already done an evo with very similar turbo/engine setup to yours then you will probably have to play around yourself.  You also need to be careful of aggressive limiting if your engine has hydraulic cam followers.

Hi Curtis,
From the info you have given I think it is quite unlikely there is an ECU issue.  It is more likely to be a failed sensor, a wiring issue, or possibly something like the CAS has moved (I think remember reading the CAS drive sometimes shears or comes loose on RB's?).  There is no volatile memory that would be lost, reset or changed by disconnecting the ECU. 
The fault codes may or may not be part of the issue, they are all related to AN/AT inputs and are often generated when a sensor has been disconnected.  So they could be just from when the mechanic was working and he unplugged a few wires or they could indicate a faulty sensor or bad connection to a sensor (they could also just be a lazy tuner that never set the fault conditions right in the first place).  So it would be a good idea to do a quick reality check on all the sensors.  A quick test of the basics would go like this: With the engine cold (after car has been sitting overnight), attach laptop and turn on ignition - eng not running.  Air temp and water temp should both read similar values and they should be close to room temperature (say about 20°C depending where you live).  MAP should read about 100KPa.  TPS should read 0% with throttle closed and 100% with foot on floor.  Those are the main ones that will influence how the car runs.  Start car and warm it up, make sure air and water temp still give realistic numbers, TPS should be the same as before and MAP should be <50KPa at idle.  If you have access to a timing light it would also be worth putting a timing light on it and make sure the timing marks show the same timing as the ECU is commanding.
Read the help file about how to do an ECU datalog and if you can do that it might give us some further clues too.

There are quite a few ways to do this but this would be my suggestion.  Your pot will be connected to an analog input.  Set the Analog input function to "Voltage 0.5V", name it something like "Launch Pot".
Set the launch mode to "3D Launch RPM table".  Put your Launch pot analog channel on one axis of the table (values should span 0-5) and usually non driven wheel speed on the other axis. My rough example below would allow your pot to adjust initial launch RPM from 3000 to 5500RPM.

Andy, yes I think you are right with a factor of 10 being at play in the mix somewhere...
Fant, another work-around you could use to get you running with realistic numbers and settings would be to switch your equation load source to MAP. Then just set up one of the analog inputs as a MAP (but you don't need to have a MAP sensor connected), just set up the error value to 100Kpa so the ecu sees a MAP of 100 all the time.

No it should not be wired in firing order. 1>1, 2>2, etc as you already have it is correct.  You need to put a timing light on it now to check your trigger offset. The reason is before when it had a distributor the offset could be out by 180 or 360 deg and it would still run fine, now with COP it will only run when you have that setting correct.  

The position of the CAS doesn't matter, it is taken care of by the "trigger offset".
You must first do the ECCS sync on the trigger setting page (read the help file), then do the base timing under trigger>calibrate.

Yes, There are some CAN receive templates in pclink already for some of the common ones; Motec LTC, Ecotrons, AEM X Series.  The CAN configuration is flexible enough to allow you to receive any CAN wideband stream that I know of if you have your eyes on some other brand. 
Also Link have their own CAN Lambda controller coming out soon if you are not in a hurry. 

Yes you can convert the map.  You need the new ecu powered up and connected to PClink G4+, then it will allow you to open/load up your old map, it will convert automatically.  Be sure to check all sensors and new tables are reading sensible.  Especially tables like short pulse width adder.

Yellow is the default wideband output on innovate controllers so would be the correct wire to use.

Yes, you should download the software and have a play if you haven't done so already:

 
I know it should work fine if your engine is a standard even 120° firing angle, however if you have one of those odd engines where one piston comes up as two go down you might have to get creative with the configuration and wiring.

Yellow is the default wideband output on innovate controllers so would be the correct wire to use.

Not sure how you missed the wiring:

Set your aux output to ISC solenoid and select a suitable frequency.  Most of the settings under Idle speed control apply to both stepper or solenoid types. 

You know this function is already built in right?  Look up help on "quick trim".  Select the cell or range of cells in your fuel table that you want to adjust, then hit "M" key.  This will bring up the quick trim dialog where you enter your measured or "logged" AFR, it then compares it to the target AFR (either taken from your target table or you can enter some different target) and adjusts the cell values to correct the difference.

Sounds like ECU hold power or maybe the anti-theft function.  Check no digital inputs are assigned to anitheft and read help about ecu hold power function so you can make sure that is set up right.
Edit: Actually just noticed in your screen shots above ECU hold power is active so that your problem.