I dunno about how swapping the engine & trans would be straight forward... And I'm not sure what model your Fairmont is (Series 1 or 2?) coz that might mean u need to figure out ways for (assuming it's a series 1) an MPFI 3-speed car's ECU to be put into a CFI 4 speed (keeping the 4 speed over the 3 speed of course!). If it's a series 2 then I spose it'd be much simpler doing the swap.
However, why swap the whole engine then taking the MPFI stuff off the Fairmont (intake manifold & fuel rail/injectors I think) & maybe the head (and replacing the head gasket with a *new* one) and putting it on the wagon's bottom end would be just fine? If you've got $250ish to spare, hunt around for an EF head & rocker cover
Either on here or the other FordForums there is a thread somewhere about CFI to MPFI conversions, as they're quite popular among EA owners.
Interior swap should be pretty simple (doorskins, seats, etc) but I dunno about electrics such as trip computer, dash, etc due to differing fuse boxes (I think).
I'm sorry that I'm not that much of a help, but I just want to warn you of the possible quibbles that might come up. Post up some pix when you're done though mate!