I just picked up a Viper and did the same thing you are doing. Here are some other common problems from my research, in addition to those mentioned above:
-Replace the pull-rope holder on top of the chain case (Yamaha PN 8FF-1546C-00-00, it's only $3.50). Yours is probably worn, even if it looks ok on the outside.
-Weld the cracks in the exhaust manifold (mine was cracked in 4 places, 2 on top and 2 on bottom).
-Make sure there is a gasket or silicone sealant under the fuel pump to keep water from freezing in the vent hole (mine was siliconed but I put a gasket under it anyway).
-Weld the cracks in the W-Arm on the front suspension (I didn't do this because I replaced my skid with a monoshock skid).
-Revalve all 4 shocks if they're stock (stock valving is terribly stiff on the compression stroke).
-Install a rear tunnel cooler (stock Vipers like to overheat). I installed an SRX cooler into mine but any cooler is better than none.
-Install the Bender / Opticool head gasket (it promotes even cooling across all 3 cylinders... stock Vipers like to overheat).
-Install an SRX engine torque limiter (the Viper has none; instead Yamaha aligns the engine crooked to the jackshaft, hoping that it'll pull itself into alignment).
-Replace the front left engine side engine mount bracket with either the SRX bracket (it uses 3 mounting bolts vs 2) or at least replace your stock 2 bolts with higher grade bolts. They tend to break probably from lack of a stock torque limiter.
-Replace the fuel filter inside the gas tank.
That's about it, other than general repair and maintenance
