Nice score on the loot. 
What is your method of assembling the lower cases?
I'm making this up and I'm sure someone can provide better guidance...
(77 550f) Assuming case is bare but all parts (gears, crank) are assembled:
- clean again. I like compressed air.
Bottom half:
- if the bearing by the oil pump is out, heat up case in oven for a little bit and it should pop right in.
- put in oil guides, etc. Mine has two, one under crank and a black plastic one.
- press in oil seal for the shift shaft/arm thing.
- pop in crank bearings
- put oil seals on crank
- optional - put hondabond on crank oil seals. no idea if this is kosher. my method is to just hondabond half of the seals as I put them into the bottom of the case. When I join the cases later, I hondabond right onto the case including along where the top half of the seal is. Either way, the seal gets a little hondabond.
- lower crank w/chains and oil seals on it onto the bearings. I use lots of lube on the bearings and because I'm paranoid.
- put starter clutch onto primary chain.
- slide the shaft that goes through the starter clutch in. be careful with the roller bearings on the shaft and jiggle it together. With my case, I always have to lightly tap it in (or out) with a few gentle taps from a hammer right at the end. The bearing should be flush with the case.
- This is a good time to confirm that your primary chain isn't touching the bottom of your case, assuming you are using an old chain.
- do the kickstarter. I always refer to my manual to get the spring/washer order. I basically put something on the table in front of the shaft to hold it in against the spring while I fit the inner parts and put on the clip. Basically the sprocket near the case should spin freely unless you turn the shaft. I think the one thing to figure out is how the outer return spring on the outside of the case goes.
- drop the two gear shafts in. Note how the holes line up with the cases so the pins/oil passages line up.
- put in the two oil seals on the left side of the gear shafts. Again, I chose to lightly hondabond the oil seals to the case.
- I prefer to put the gears and shift forks in neutral for when I join the cases.
top half:
- put in the alignment dowels
- pop in crank bearings
- I think the drum shaft has an oil seal on the small end, I forget there. Maybe not.
- slide in shift drum, putting in the big fork as you do. Note how the fork goes- basically the side with the pin will be to the rider's left when it's all assembled?
- Drop the pin in the big fork and I use pliers to push the clip in that retains the pin.
- slide in the rear shift fork shaft, putting on the forks as you go. if you're unsure of which forks goes on the left and the right, put them spin the shift drum while holding the forks up to note how the motion should go. If you have it wrong you won't be able to spin the drum properly.
- put in the starter gear. you can see in my photo above how it goes - the teeth of the small gear line up with the shaft in the bottom of the case when you look at it.
joining:
- wipe off case mating surfaces (I use acetone)
- assembly lube the crank bearings, etc again
- very light hondabond all around. I prefer to do the top case, not the bottom, just for visibility.
- I do not know if you are supposed to HB the towers that hold the crank in, assuming there might be an issue there with crank bearing specs. I split the difference and did an extremely thin coat on those towers.
- I generally barely HB near the clutch side, since oil leaks are a non issue there. I do put HB where the crank and tranny oil seals will sit.
- start to drop the cases together. I position the rods vertical but they often fall. A helper would be nice there.
- at this point the shift forks are probably stopping the back of the case. look in there and you'll probably have to push the inner big fork into it's slot.
- it should drop together more.
- Make sure the two tranny bearings are aligned. There is a metal half circle clip thing on each that that fits into a groove on the upper case and on the bearing. if it's not lined up, tap it left and right until the cases drop together more.
- If things still aren't flush, it may be that the little pins at the end of the tranny shafts aren't lined up with the holes in the cases. again, jiggle things.
- Things should be flush now. I start threading in the case bolts on the top just finger tight and then tilt the case and do the ones on the bottom. If I recall the manual has you do the crank bolts first, then all the little bottom bolts, then the top. I'd refer to the manual for the crank bolt order and all the torque specs - I got it off of this site and can relay that part if needed.
