Steph, I had a chance this afternoon after posting to check some books.
Kirkland's "The Locomotive Builders - Volume 2 (Alco)" says that the FPA4 (and also the FPB4 B-unit) was six inches longer than the FA2 (FB2). He DOESN'T say that the increase is in the carbody proper, and I would think that six inches COULD be the result of changes in coupler shank and mounting, BUT: (1) The 12-251 engine is a bit longer than the 12-244 and (2) the FPA4 has at least one more bit of internal equipment than the FA2 (see below), so it may be that the designers "stretched" the carbody to accommodate. (Maybe the exact angle of the diagonal truss members in the carbody structure isn't too important?)
Steinbrenner's "Alco - A Centennial History" confirms that four CN FA2 (well, technically, two FA2 and two FB2) were rebuilt with 12-251 engines (and the leftover 12-244 went into the RS24 units). He says, however, that the rebuilt units kept the FA2 configuration of air compressor aftercooler: a zig-zag of pipes mounted externally on the rear wall of the unit. They therefore would NOT have had the main FPA4 spotting feature: the extra vents velow the radiator intake shutters, which are for the compressor aftercooler.
So I'm not sure what to tell you. Good luck with modeling (and if anyone turns up more dimensional data, I'd be interested to hear it!).