Sorry, I forgot about this post.
We tried lots and lots of different latency settings, both positive and minus. The best and most efficient result coming from a setting of 1.6ms and 46% injector size difference (injector size obviously not the issue here). It is still injecting fuel for too long however this setting gave the best result. This was all while on the dyno. AFR's were all healthy at this setting. I am keen to get it back onto the dyno and try 1.07ms again.