So I had this EXACT problem with my VEC2 on my Gen3 for the past couple weeks... I'm still a Viper noob, so I don't know if the Gen2 is installed the same... Forgive me if I'm wrong!
The car would sometimes throw the CEL with a CKP/CMP code, sometimes not, but it would stumble HARD under WOT and 80% OT, and for a couple mornings it would run really rough for the first 30-45 seconds... I decided to go in fully armed, so I picked up a new Cam sensor, Crank Sensor, and Fuel Filter ('03 with 55K miles, probably has the stock filter, and I heard it is a BEAST to change). I called Sean Roe just to get his perspective on the VEC2 and in 5 minutes, he told me exactly what I was looking for. The VEC2 installation requires intercepting the CKP sensor. Before I started mucking with sensor replacement, I looked over the loom and found the connectors for the CKP sensor. I have used far better connectors in my old car stereos... these were in awful shape. I pulled the wires apart and cleaned them, and the car has been 100% ever since. I feel like a tool for not checking that before, but I have a fresh cam/crank sensor when I need it, and I have the fuel filter set aside for a nice winter project.
Sean told me how easy it was to bypass the CKP sensor and how to bypass the VEC2. It is really just plug and play. Definitely found that unplugging the CKP wire while the engine is running will kill it in a heartbeat.
Hope this helps, it may be the same problem... If not, maybe this will help someone else.
-mb