79 TransAm w/301 and 4-speed. I swapped out the 301 for a 400. There are a quite a few allignment/clearence issues due to the fact the the 400 sit's about 2 inches up and forward. The driveshaft yoke only goes about half way into the back of the transmission. Get a longer driveshaft, or have this one lengthened? I've never delt w/them before. Also, are adjustments to the shifter linkage necessary/possible?

A good driveshaft shop can make up a new longer tube using your ends. If the shift linkage reaches you may be able to get it to work, this is trial and error.