In reading this thread through, it sounds like the key issue on getting a new locomotive is the condition of the track. BTW, what kind of rail is on the A&A? 70lb? More or less?
As for parts, you say that GE still makes everything that's on them -- I sure hope that you have a good parts catalog for a 44 tonner! Ever try doing business with Logan? Unless you know what the part number is, don't even bother picking up the phone to call them (their people in customer service are worthless). Like I said before, trying to find parts for those old Cat engines in the 44 tonners is next to impossible -- a key reason why railroads that have been operating these things for years are giving up on them. Take the Claremont & Concord for example. They've basically had it with trying to find parts for the old 44 tonners so they're selling them off.
As I stated before, the GE centercabs are historic to the railroad, however the "charm" of the locomotive doesn't pay the bills. If the A&A ever hopes to grow and expand its freight business, it needs to develop a plan for the replacement of those locomotives. I would not go out and buy a 539 powered Alco for the save reason, that parts are hard to come by. A 251 powered S6 or T6 would be good, but good luck on finding one. I think a SW1500 would be perfect for the A&A, unfortunately the price tag on EMD switchers is ridiculously steep. My personal favorite would be a GE U18B, but again, good luck on finding one. Of course all of this would be contingent upon whether the track could carry the weight of the locomotive. Yes, larger engines use water instead of antifreeze, but if you have a heated engine house, what's the problem? If you need to install a layover system, a custom system can be installed relatively cheaply. Two years ago I installed an oil fired boiler on a U23B to be used as a layover system. Price tag for the system was about $1500.
One final thought, the Rochester & Genessee Valley RR Museum has a beautiful US Army 80 tonner. Thing looks like a brand new locomotive -- its got 26 air, MU, the works. While I certainly can't speak for those folks, I would bet that they would be interested in preserving an A&A 44 tonner. Perhaps a trade could be worked out? Merely a suggestion (Otto -- don't shoot me!)