More labor involved, parts requirements to drop in an FE may not be a large factor. In this case, new hearders anyway, personally I'd go with a new clutch as well for either setup. Motor mount expense is not a big factor, getting the motor mounts installed or modified could be an issue. Get it right and you could likely keep your current drive shaft. Certainly more "brain work" required.
Oil pan, on either engine, could also be an issue. Road racing pan could set you back $500 easy enough so in either case it's not to be taken lightly.
A rare bird, FFR with an FE, you don't see those much. Re-sale value increase alone may justify the extra cash.