390 into a 56 truck
One of the things you are going to have to do, is find a truck rear sump and oil pump pickup. The other thing you will need to collect is the oil filter mount from a truck FE engine. These pieces are plentiful, so it is no big deal.
I can't remember whether the front mount points are the same for the Y engine and the FE, I know there were differences in how the mounts attached to the block between the earlier and later FE engines. I believe the mounts will match up to the Y engine mount points. The 68 engine will have the later pattern. I just can't remember but in any case you have lots of room to place the engine properly.
Don't screw up the exhaust manifolds or toss them, If they are original, they are the GT manifold with the staggered bolt pattern instead of the bolt holes at the top and bottom. The headers you buy will have to be for the GT heads. They are excellent heads, so don't exchange them.
I also agree with your decision to use the C-6. It is a great transmission and saves all the headaches of matching bellhousings.