Tony-
To answer your questions:
1) Chances are that you will get a check engine light with a 'primary cat failure' code.
2) Your car will also surge at light throttle rpms which tells me that it does effect the computer at light throttle loads.
3) It should not make your car go into 'limp' mode which normally makes it run rich. This is usually caused in 99+ Vipers when headers are added and another code is triggered; the 'heater warmup failure' code. If you are using stock headers, you should be fine
4) Your MOPAR PCM MAY fix the problem, and then again, maybe not. There is a reason why MOPAR stopped producing these and went through a few different production runs. It's becuase they were having problems with its performance, consistency, and reliability. We tested a few on cars and found that it caused a loss in power, higher/erratic idle, and cars seem to run hotter. Others have had different results with similar symptoms. However, it did seem to cancel out the check engine light. BUT, if you are removing the cats to increase power, you may find that the MOPAR PCM cancels the light, but robs you of more power than the cats are adding.
5) If it doesn't work, let me know. We offer an easy remedy kit to cure the problem. We have sold over 40 sets of our APEX Snake Boxes kits to VCA members so far. They are specifically designed for the Viper to cure the problems caused when you remove the cats. Installation takes only a few minutes as our kit includes the boxes with Viper connectors and soldered wires for a snap-in installation, stainless oxygen sensor plugs, tool for installation, instructions, etc..
Good luck!