Go for it Dave, it'll be great seeing what you do with it! I've had a soft spot for the Rutland for a while - I was a member of the Rensselaer Model Railroad Club which had the New England, Berkshire, & Western Railroad (based on a combination of the Rutland and D&H).
With a Dremel and a good sander, removing running boards shouldn't be difficult, but it's a big psychological step - I've avoided a few projects for this reason in favor of lower hanging fruit. Whatever route you choose, the payoff will be magnificent - those green boilered Mountains in the Green Mountains look sleek.
As for my own project, one step forward one step back. Unable to find a suitable tender in one piece, I'm piecing one together.
The Good: Lionel has available on its parts support site an entire Mohawk tender frame with almost full electronics package - the only thing missing is the RS5 audio board. I picked one up, and put the RS4 audio board from the engines original tender to check it out. Sound functions as it should, but I cannot get electro couplers or a backup light without a proper RS5 audio board. Just another misc. item to keep an eye out for.
The bad: The coupler was damaged in shipping. I emailed Lionel and asked for a replacement.
The ugly: When I opened up the original tender to remove the RS4 audio board, I found this wire that had been pinched between the tender shell and frame for 22 years. Hasn't failed yet, but another thing on the agenda to fix.
~Chris