The exhaust will help, but it's all going to boil down to the weak link in the entire system as a whole. Doing the CatBack will open up the last half of the system, but the headers will still be restricting the flow. Once you do the headers, you still have to get it breathing better on the front side of the flow to really see a big change.
I wouldn't worry about the engine handling it until you start to think about pressurizing it (super-charging, turbo-charging or nitrous). The gains are minimal (but still fun) until you go into that area of mods. With only 450 HP (on a good day) in my Gen II, I have to wonder about boosting it and the value added to my overall experience in the Viper. I don't track it much and I'm still learning to handle what it's got STOCK.
We all want the bigger bragging rights, but really, where does it all stop?
With my last sport bike, my tech asked if I was using all the power with what I had (I was in there to hop it up and boost the HP) ... decided to NOT spend the money on something that I couldn't use up to the top.
Isn't 600HP enough to learn to control? Get out on the track and if you STILL have to go for more, do it and run in the Viper Cup.
If you want to do the PCM, check into Viper Specialty for their SCT tuner and software... team up with a good tuner in your area and go for the gold! Get ready though, you're about to enter into warp drive with cost and time on your new toy.