Some of the gurus can weigh in with more authority than I and you can check some of the AT forums (clickclickracing.com for one); but from what I understand, the method they used to get the fifth gear is what reduces the torque rating (700 ft/lb vs 550 ft/lbs). I considered going with the 5R55 but am going with the 4R70W for that reason. As Pete said you'll have to have a trans conttoller and a shifter. At this point I'm probably going with Baumann Optishift controller and Lokar shifter.
If you go with a carb, you'll need to get a Throttle Position Sensor (TPS) signal but a kit to retrofit one to a carb is available. I'm going with an aftermarket EFI system for my 351W so the TPS signal isn't a problem. I'm not familiar with the mod motors but I'm sure there are some things unique to using them but again there are some gurus available to help out. Arrowhead has a good site with pics of his build that might interest you.
Good Luck, keep us posted on your progress.