Bit of an update,
Firstly swapped injector 2 and 3 over and recoded.
This made no difference to the misfire or vagcom readings.
Then checked compression, didn't seem too bad at 300psi.
Then dropped a set of verniers down the injector hole to measure the top of the piston. Cylinder 2 where I'm getting bad readings from is 2mm lower than cylinder 3. Re measured multiple times and had a few people try and always 2mm lower on cylinder 2.
Would 2mm be enough to cause the strange internal moment readings and such a bad idle and misfire but fine when warm? Guess it's a slightly bent rod on cylinder 2