2009 gmc 2500hd

Hi we try to tune a 2009 2005HD with 6.0 liter ecu e38 the got ported heads and vortech supercharged on it and they are stroke for 6.6 liter injector was supposed 60 pound. We tune 2001 pick up with no problem but the e38 look very tricky to tune.
1- wath is the best way to tune them just maf or need change ve table also
2- wath is the best procedure to doing the adjustement.
Because i try little bit but the engine goes very bad the all time he goes in reduce engine power mode sometime they rich sometime came very lean they are crazy and also he got an automatic transmission on it T43 it`s downshit all a time on the dyno.
We are buy the CD from Greg they help little bit but the e38 we dont know how to work with.

Thank`s for reply:wallbash: