The HP Tuners editing suite is very good software. As stated by Tweeder, for a manual trans you disable (uncheck) all of the DTC's that are associated with shifting the automatic. If the PCM doesn't look for them no fault codes will register. You also uncheck any codes associated with things that are not used on your swap. If Dan supplied your PCM, he well knows all about the process. As for dyno tuning that is a science in itself and the final step. I would first get the car up and running properly and go from there..
" THE BLACK PARALYZER" -87GT 3800SC Series III engine, custom ZZP /Frozen Boost Intercooler setup, 3.4" Pulley, Powerlog manifold, Northstar TB, LS1 MAF, 3" Flotech Afterburner Exhaust, Autolite 104's, MSD wires, Custom CAI, 4T65eHD w. custom axles, HP Tuners VCM Suite.
87GT - ALL OUT 3.4L Turbocharged engine, Garrett Hybrid Turbo, MSD ign., modified TH125H
" ON THE LOOSE WITHOUT THE JUICE "