ClintBHP

Sorry conversion error, try now.

Yes I have seen twice where we have start issues with CAN that they were ok with a roll/bump start. - It narrows the search down

Try this: Select the correct CAN Bus and Enable User Defined Mode and Transmit Generic Dash at 1Mbs on CAN ID 1000
 
 

What are the errors exactly, is the Dash terminated?
If you put a multi meter over the can bus while everything is turned off what is the resistance. 
Are the 2 CAN wires twisted together at a rate of about 1 twist per inch?

You are transmitting, your transmit counter has hit 128 and not gone up more this indicates the Plex is not sending an Acknowledgement (or cant see the transmit) 

1. Your 'Engine Fan 2' does not seem to be set up on any inputs and is set to come on at 0 degrees so will always be on ? You have Engine Fan 1 and Engine Fan 3 set to Ignition Drive 3 & 4 
2. Your MAP has the default Throttle Settings, you will need to perform a calibration before the throttle will work properly.
3. Your Lambda output seems to be stuck at ground, you will need to check the wiring, and if correct measure the output of the AEM with a voltmeter. What AEM part number do you have.

1. When you say play, what ECU output (pin) are you trying to control ?
3. You have a Gauge, that reads ok right? You have wired the White wire to An Volt 6 on the expansion connector. 
If you dont have a voltmeter you can use the ECU, set the AN volt Input to Voltage 0-5v and check the input voltage on the configuration screen.
If that reads 0v then humour me and try to move it to AN Volt 5 (the next pin on the expansion connector) and see what that reads. 

Fingers crossed my friend 

I would use it as a chance to start using Lambda, even if you have to print a little chart out to reference for a while, with modern fuels containing more and more ethanol its wise to think in Lambda terms, even though AFR might seen easier due to the swing of the values.

As you self answered 3 & 4 :
 
1 - Set your engine protection rpm limit to Ignition Cut.
2 - Have you checked the CAN configuration  - ECU Controls - CAN Config

I think the V88 is effectively a Link G4 Xtreme then you can do the following:
1. Download the latest version of PCLink and connect your new ECU, upload your old map file. (this does not work offline) 
Upgrade the firmware
Check all the inputs and outputs are set correct.
2. Always worth doing but should be fine.
3. You wont be able to run the car with a locked ECU.

Think this should work:
Setup 2 Virtual Aux
Virtual Aux 1
Logic = Cond(1 AND 2) OR 3
SW Cond 1 ECT | > 55
SW Cond 2  | Aux Virtual Value1 = ON  | 1
SW Cond 3 | ECT > | 75
Virtual Aux 2
Logic = Cond(1 AND 2) OR 3
SW Cond 1 IAT | > 35
SW Cond 2  | Aux Virtual Value1 = ON  | 2
SW Cond 3 | IAT > | 50
Then setup a AUX as a GP output 
Switch Logic Cond 1 OR 2
SW Cond 1 Aux Virtual Value1 = ON | 1
SW Cond 2 Aux Virtual Value1 = ON | 2

Yes I know but it was unnecessary, and he has now lost the ability to go back to OE system should he want to sell the car or engine at a later date without buying an ever getting rarer engine part.
 
All the WRC Cars I am looking after nearly all have Link fitted now, and I have also helped a few other dealers configure theirs.
 
I know I am correct and I know what your trigger decoding is doing, it is not clearing the IRQ Flag on trigger 2 until the missing tooth on trigger 1 is seen again. The trigger wheel the user fitted is from Turbosport, I have fitted a Monsoon to a customers car with the exact pulley installed. As long as there was not a manufacturing fault the missing tooth will be in exact relation to the woodruff key on the crank shaft.
 
Where are these massive errors, the massive errors I was told was from running the RS500 Trigger in software with the 36-1 wheel fitted,
His post said above "I spoke to Clint at bhp and he said just set the triggers to ford duratec as that uses a 36-1 trigger and 2 point cam ? Rather than using the rs500 triggers. I tried this and it run better. Not sure what’s best "
His problems are not the pattern but more likely to still be trigger setup in software, static timing, hardware or wiring. Given 20 minutes with the car I would be able to have it running perfectly.
 
Work I do is never luck, this is a kit I sell a lot of and it works every time perfectly, fully sequential ignition and fuel, no trigger errors. 

Not seen one, just need to do it the hard way with 2 timers and 2 virtuals and dual tables. 
Would be a nice addition though, I do actually get asked this a lot from the cruise and show guys and gals who want flames and pops at the weekend.