I just built my 951 carbed. (same idea with internals, but slightly different parts) The hardest part is cleaning and prepping the gasket surfaces. It took me a whole evening (4:30-10 (with supper break) just to clean everything. I used an angle die grinder with the 3M gasket surface prep pads. They looked brand new when done. Thats the only way to do it IMO. A knife or scraper gouges the surface and are prone to leaks.
As for aligning the crank/ counterbalance, its just 2 gears. I would say the hardest part is manipulating the crank and getting the internal crank seals in their slots without pinching or tearing them. Racerxx suggested I use Threebond 1211. Fantastic stuff. Sealed my case perfectly the first time. Then drop the base gasket on. Install pistons. (all easy) Then it helps to have 2 people to wrestle the cylinders over the pistons. One of the hardest motors i've worked on. Just as you get one in, the other pops out or you catch a ring so go slow and be careful. Put the studs in and play with those stupid O-rings. Then toss the head/headgasket on. Torque it down evenly, and you're set.
I did a near OEM build (only things non OEM were piston rings and gasket kit from WSM) OEM crank, rebuilt OEM counterbalance shaft, OEM pistons came just around 850$ maybe a little more (including shipping). So if you want to do a quality build yourself, its well worth it IMO. Because good parts don't often fail. Its the cheap cranks that will get you. Or a bad hone job that catches a ring.