IIRC power levels must be above 11.9v at all times, I think you have something like 200-400ms before you "nuke" the PCM if these conditions are not met. I know a guy who can repair the OBD I PCMs though incase something goes awry.
Tunercat also turns on the FAN #1/#2 relays, when LT1 Edit does not, so I used to unplug my relays before getting down and dirty, to save battery.
Turn your key to the ON POSITION (dont start the car of course), wait about 10 seconds for VATs to do its things (not sure how that will work with a VATs bypass), and then you can read or write to the PCM. This should take about 3 minutes, dont interupt it, make sure there is no powersaving on the laptop etc
Most guys that write the editorials talk about LT1 Edit, the terminology is different but if you know cars you should have no problems, I can 'translate' if need be for anyone.
http://para.noid.org/~lj/PCM%20Tutorial/PCMtutorial.htm
http://www.bfranker.badz28.com/LT1Edit/LT1files.htm
(good explanation of the sensors etc)
http://members.aol.com/InjuneerZZ/ScanMast.htm
http://www.wotelectronics.com/cables.html
http://www.carprogrammer.com/
There is an email list too, www.lt1edit.com The Tunercat list is usually pretty dead, but again its the same thing other than terms used to describe fields.