If you do an engine swap, the PCM will not allow you to start your car without the proper VATS inputs. Since a swap doesn't use the VATs feature it must be shut off in order for the car to start.
From Chris at HP Tuners. (Using the VCM tuning suite editor):
To disable VATS you must do the following:
1. Set the VATS value to "PWM"
2. Set DTC P1626 to "3 - No Error Reported"
3. Set DTC P1629 to "3 - No Error Reported"
If you have problems please email your file to support.
Chris...
I checked my PCM and it appears that the above solution worked but judging from Chris answer this may or may not work on your PCM. In any event it appears that HP is willing to help us obtain the right code to disable the VATs feature.
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87GT - 3800SC Series III engine, 3.4" Pulley, N* TB, LS1 MAF, Flotech Exhaust Autolite 104's Custom CAI 4T65eHD w. custom axles, HP Tuners VCM Suite.
87GT - 3.4L Turbocharged engine, modified TH125H
" I'M ON THE LOOSE WITHOUT THE JUICE "