The bell housing should go onto your six speed with no problems. Since the transmission is built, you will either need to swap the pump or move the modified pump valves/springs/shims/whatever your builder did from the old pump to the new one. It's easier to just swap the whole pump/separator plate assembly. Remove all the bolts inside the bell housing, and the pump will drop out of the bell housing.
I'll tell you right now, it's going to be a PITA to change that rear adapter plate with the engine in the truck. It's made to go on before the oil pan and has dowel pins that line it up to the back of the block and the upper oil pan. You will need to remove the lower oil pan to get out 4 bolts that go through the upper oil pan into the flywheel housing (3 go through the inside and one is on the outside). You also have to remove the flywheel bolts (very tight!). You will need to remove the turbo drain nuts and studs (this will allow you to leave the turbo in place). The coolant elbow that goes from the oil cooler to the flywheel housing will also need to be removed. If you pull the rear main seal, it will probably get you a little more room to work as the flywheel housing is coming out. To get it out, you will have to pry the top loose first. Once you get it back far enough to clear the dowel pins in the back of the block, you can pry it up to clear the dowel pins in the oil pan. Once you get it off, you'll need to pull the little metal sleeve off the crank that is part of the rear main seal. With the new housing on, you'll need a tool to install the new seal. Good luck with it.