This topic has been gone over many times before. Check out RYPN.org & you will get a different view on the replication vs restoration vs original debate.
BTW, the RMNE 4K loco (4096) was done as an exercise in cosmetic restoration, to reproduce the New York Central colour scheme. That decision was made because the Union Pacific was deemed a little too distant to affect view visitors with something they could relate.
(Yeah right. The decision was made because the New Haven did not have an E-unit & NYC was next door - B&M need not apply (^|^). ) This was done during a major change of focus and activity for the then CVRM. In hindsight, the Museum came to the realisation that while result was spectacular, the reasoning was not that of a museum - a mistake had been made and will not be repeated. UP colours would have been just fine and painting it AMTRAK would have not been too shabby either.
I am quite familiar with the Berkshire group and I know their standards.
The Alco will be a great addition - a working condition RS3 is hard to find nowdays and is quite impressive to the general public just idling at the head of a train - almost as good as steam!
However, if I may add in my thoughts and they are just mine and hopefully will be taken into the mix for an ultimate decision, here they are:
Railfans do not pay the bills - all they want is pictures and give the dreaded 6 words "all you need to do is....." - they are not your audience. The general public is. (Railfans - not those who show up for work or donate in other ways (they have other appellations) - don't get your knickers in a knot...).
There is a great debate as to "using up your irreplaceable assets". Are you going to run that Sou PS4 or have it preserved permanently as a static display. Each has its points - the U.K. does a tremendous job of operating their steam locomotives (and a Deltic) as well as having York.
A replication is just fine if the fabric of the object is not destroyed in the process. New Haven 562? Sure, but you have to tell that story to the public AND it benefits the museum since there are 3 stories involved here; the original artifact, the (physical) replication story and the story why to replicate, i.e. the Berkshire Line of the New Haven. Without a prominent and thorough display of the replication process - you are lying to the public (and most railfans and NHRHTA members would mutter "ah, the New Haven never owned one" or to paraphrase Utah Phillips "My God, it's moose turd pie! - but it's tasty!".
Restoration - a fine story here as a B&S or a Cee-ment plant industrial loco. OK - maybe the paint jobs aren't as snappy, but the story is real and the history is there. Again, the public will appreciate the effort - and you can work in the Berkshire Line story into the narrative.
Restoration II - adopt a Berkshire Scenic paint scheme & apply it. If it evokes the New Haven scheme or Penn Central only a small fraction of the General Public will give a whit (Maude, Maude - this thing looks just like the olde Penn Central - wow! what a rush a flashback to the '60s...). But the GP should be informed as to what the rationale for your decision is.
What is come down to is this: This is YOUR museum and as such you have the responsibility to preserve the artifacts in your possession and present them to the public in a manner that fits the mission of the museum.
I assume that you have a mission statement and a accession/deaccession policy. If the RS3 fits the scope of collection then you have additional obligations as a museum, if not, it is cannon fodder (but may be in someone else's scope of collection).
Be prepared to defend your decision as best as you can, especially if it is controversial.
Look to other operating and non-operating railroad museums for guidance - see what and how they do and present themselves.
And finally, take everything said here with a mountain of salt.
Good luck, call me when it's up & running & I will bring a camera....
If you can't dazzle them with brilliance -
Baffle 'em with bulls**t...