I am sure you already read all of the options and tried this but...have you tried disconnecting the battery for a while then reflashing it? I just had one mess up during a flash the other day. It was my first time going through that. It would not start, would not connect with HPTuners, would not connect with GMs SPS system for a fresh flash... After a battery disconnect all was fine. It took the next flash and works great now.
Maybe upgrading to the newer PCM is not really needed. Well it does function at roughly twice the speed and offer better VE tuning... AND... it is totally possible. Just found this:
http://www.corvetteforum.com/forums/...-corvette.html
Apparently you will just need to turn off some evap codes that Vettes did not have until later but your can leave your 1998 codes functional if you like. There may be a few other little details but if you are running a pair of turbos this upgrade could be TOTALLY WORTH IT. Enjoy!