As another mustang guy, welcome to your search for another snake car. I just moved from an '11 GT500 to a '14 and have had 11 mustangs, so you're in good company.
I've had gen2, 3, and now a gen4. For gen3 I prefer the 03 for modding and it's internals, otherwise I'd say go '05, it is built in a couple yrs of proven line assembly, etc, and if you get to an '06 you might be paying enough to wonder about jumping to an '08 gen4. I'd think you'd want to potentially mod it so youre looking at the right gen of viper for that, you're used to a lot of power and the viper is geared tall, so it'll feel a little lazy compared to the modded GT500 on power, so I'd see you doing a few tweaks like I did to my gen3.
Things to look for IMO-
Check all tires for equal wear, I've seen an unusually new tire on a corner which is a problem in handling and could even indicate they nailed a curb or something.
Check for any signs of seal leakage from the struts, which is not uncommon on gen3s.
Once you're ready to buy a particular car and can drive it, do a wheel spin take off, check for overly dramatic shake in the shifter, which can indicate a broken or worn trans mount or engine mounts - vipers can go thru mounts in 10,000 mis if driven the way they were meant to be. There are great replacements but good to know if you have to pay for this upfront.
If you have one in the area of the car, it'd be well worth it to pay for a viper tech inspection.
Play with the windows, the regulators are another weak point and pricey, the windows should operate perfectly, if they don't then it'll cost you later.
Good luck with shopping, it's part of the fun. If you find an 08 gen4 in the upper stretch of your price range, it might be worth considering, for the extra 95 HP and the awesome rear end / diff improvement as well as a few smaller items.
Dave.
And not to leave out, a fair number of dealers and vendors here are more than helpful as well.
