Hmmm... interesting. You could get a cracking guitar, but you could easily end up with two guitars that don't seem to have the magic of either. You'll only find out by trying.
You're talking about a CIJ/MIJ custom? I have one hanging right next to my Baja, and I know exactly what you mean about the neck, but I find I can get used to either.
Finish-wise, the Baja is thicker (I think) but, still, I find both of them feel a bit plasticky compared to some others in the arsenal if I start thinking about it. They both get played less because of it.
I've never considered swapping the necks - a maple board on the custom just wouldn't grab me - but I do find myself wondering whether the custom would sound as good as I think it does now if it had the big maple thing attached to its alder body. I might like it, but I do value the smoothness it has now compared to the brash Baja.
Another thing to consider (over fitting), and don't quote me too much, I'm not at home to look and this is only a recollection. I seem to recall reading (probably on tdpri) from some guy that's got loads of them, that the Baja neck sits further out of the body than many teles, and the angles on the bridge are a major factor in giving it the mojo that it's got going... Is this because the heel is deep or because the Baja neck pocket is shallow?
And, er, well... to me the two guitars are what they are - I know they're designed for replacing bits etc - but I probably wouldn't bother spending two sets of strings and the time required (and the possibility of not being able to get back where I started) to find out if I like the swap...
But remember, I'm lucky enough to be able to play any neck length/radius/profile/frets and not feel too much of a shock. The only thing that really affects me adversely is if the action is too low for me (frets do come into play here, I guess) or the strings are too light - those are usually more adjustable, though. So I haven't really got the same reasons as you do for wondering about it....
