Which bolt holes aren't lining up- - - -top or bottom? I've never seen a car/truck trans that wouldn't swap, unless it was a pre-1953 car bellhousing. The 1954-up cars and trucks, 3 and 4 speeds, are supposed to have the same bolt pattern. The only difference is in the transmissions- - -trucks have threaded bolt holes at the bottom while car transmissions have threaded holes in the bell housing and the trans bolts in from the back with 4 bolts. You might be able to drill the threads out of the car bellhousing on the bottom and not have to swap.
Jerry