RE: Manual Transmission?
Anything can be done. But sometimes there are reasons why it isn't done.
If you can find an M5R2 out of a Thunderbird with a 4.6 (if they were ever made), then you could relatively easily adapt it to the Mark. However, that would be stupid, because those transmissions suck (i know two people with them, both have no synchros going into second, one has broken 3 shifters).
If you can figure out how to hook up the clutch and fabricate a new shifter that puts the stick where it needs to be without hitting the trans tunnel, then a T56 out of a Cobra could be made to work as well. But it ain't gonna be cake. Find a 4R70W and a T56, bust out a tape measure, and see what has to be done. Plus you'll have to figure out what to do with your console.