With a few exceptions (such as 489), I think the evidence is that the C&TS has done a pretty darn good job of preserving the railroad's historical "versimiltude" (anyone got a better word?). Let me try to make the case by looking at the three categories of the railroad that involve historical assets: Structures, Historical Rolling Stock, and Revenue Equipment.
STRUCTURES. This is the one part of the railroad that the SHPO's really comprehend. SHPO's are not railroaders, they look at the C&TS and see buildings, bridges, viewscapes, and cultural resources. The Commission, the Friends, and the SHPO's have collaborated well over the years on the historical preservation and rehabilitation of the railroad's structures, and all the work done on these structures conform to established federal standards. No problem here, just a tedious process that requires lots of documentation.
HISTORICAL ROLLING STOCK. Dealing with this category has largely been delegated to the Friends as the museum arm of the C&TS, with final approval by the Commission and oversight by the SHPO's. But the SHPO's do not have expertise or a basis for judgment when it comes to historical railroad equipment. So any problem someone has with rehabilitation of a piece of rolling stock ought to be directed to the Friends. To the best of my knowledge there have only been isolated cases of errors or mistakes. This is not to say there are not honest differences of interpretation (such as having one rotary painted gray and the other red), but that will always be so.
REVENUE EQUIPMENT. About the only time this category becomes a problem is when a piece of historical equipment is used in revenue service and is, by contract, under the control of the operator and its employees -- 489 being the instant case. Neither the Friends nor SHPO are involved, and I'd suggest that's the way it ought to be. Yes, I think 489 is garish, and I'll probably mention it to the management at CTSMC at an appropriate time, and you guys can do the same. (Of course, my preference is for the "bug" herald, but let's not go there).
So are there any other examples of historical "artifacts" that are not being handled appropriately by the Commission, the Friends, CTSMC, and SHPO? I don't mean instances where honest differences of interpretation are possible because of the different eras of the railroad being represented, but I mean out-and-out errors. Other than 489 and the inappropriate paint job on MW02, what else?
Let's at least try to truly define the nature and scope of the problem, if there is one, before attempting to recommend solutions.