I was thinking about getting my Viper tweaked since it is the fastest prop I have tried(even though it's not in good condition at all! ) but I noticed a couple rough spots toward the bottom of two of the blades. They amost look like "metal scabs" if that makes any sense. Here's a a pic.

If you are referring to the two white spots in the pictures they could be cavitation burns. If that is indeed the case then you need to explore your water flow and make sure nothing is disturbing the water flow to the props.

Julie

I can't remember if you are in salt water. If it isn't cav. burns, it may be salt or mineral build up also caused by cavitation.

Is it into the stainless or on the surface?

Julie is referring to speedo pick ups, transducers, etc. If nothing is in line to the flow to the prop, it could just be the hydrodynamic combination of hull drive depth and prop geometry.