Basically, what you're problem seems to be IMHO is that you have a really good turbo but half the parts you need to see the power from it. I am surprised you're tuner even tried to tune it as it sits. you have a very restrictive stock up pipe and inlet paired with a big intercooler system and a downpipe. You are replacing a turbo that flows 38lbs per min with one that flows 49 lbs per minute and only replacing half of the parts that the turbo bolts up to.
Get an up pipe, external wastegate, and a perrin turbo inlet. also if you were running a bigger top mount you would see much faster spool with that turbo than with the fmic (i used to run a 1.5xtr). TGV deletes would not hurt either.
if anyone thinks i am off track here let me know