Your best bet will be to remove your current engine and transmission together, then put your current manual transmission on the new long block. Leave the bellhousing on the manual trans, no need to remove it from the transmission. Separate your manual trans from the bad motor by removing all of the bellhousing to engine block bolts, it should then slide out of the crank. Remove clutch, flywheel, and pressure plate from the bad motor. Do all these same steps to separate the auto trans from the good motor. You will need to remove the auto transmission's pilot bushing from the new block's crank (the auto and manual pilot bushings are different sizes I think). You can rent/borrow a puller from your local parts store. While everything is apart, I would replace the clutch and pressure plate if they look at all worn, resurface the flywheel, install a new pilot bearing for the manual trans in the new motor, replace the clutch throw out bearing, then bolt everything back together. I believe you will also need to use the manual transmission dust shield that goes between the block and bellhousing, they are different between the auto/manual if my memory serves.