1) With both the engine and midshaft removed install pump with bolts snug, but not super tight. Look inside the engine compartment at the drive shaft sticking through the hole. Your goal here is to get that drive shaft to be as dead center in the hole as possible. You do this by adding shims to the two rear mounts of the pump. Never add shims to the front two mounting points of the pump. Once the shaft is a dead center as possible, install the pump with all cooling lines. Your done in the pump area.
2) Slide the midshaft onto the drive shaft. Push it as far on as possible. If there are any gaps between the mid shaft and the bulk head, add shims to each side accordingly to fill up the gaps. Because there are no bolts installed there will some gappage no matter how hard you press it on by hand. If there is an even gap all the way around the mid shaft, then no shims are necessary. Once gaps have been filled by shims, bolt the mid shaft on.
3) Next is the engine. Slide the engine into place WITHOUT the rubber damper. The first stage here is to try to get the engine height figured out. Left and right alignment is negligible at this point. You want to add shims accordingly to each mount so that you can take a card and place it on the top of both couplers and have that card sit even.
Once you have that figured out, remember or mark the position of the shims, pull the engine forward, slide in the rubber damper, add your shims back, and just barely snug each engine mount bolt. You'll now twist the engine so that when you place a card on the sides of the couplers, the card will sit flush on both sides. You can also use a variety of measuring tools to determine whether each side is aligned properly instead of a card. Between each movement remember to snug atleast one bolt back down before you let go of the engine, otherwise you'll just loose the amount you have moved the engine. Once left and right alignment has been figured out, torque down all your bolts.
4) You're done. Drink a beer. And remember you should have installed all these bolts with anti-seize.