Yes the clutch tube MUST be positioned correctly at the rear, particularly the distance to the transmission, front not so critical. The wires are usually an added harness, trace them, you can most likely remove them and reconnect the normal starter wiring. If the return line is the only reason for a gas tank swap you can tee the return into the single outlet tank, but it's still a good idea to swap the rubber lines and filler neck hose in there while the engines out.
Enlighten us as to why you need to change out the auto trans.? They don't work too bad and really open up the market if you decide to sell it.