Update;
I think I got my cases suitably surfaced and smoothed out. I ended up after some extensive checking with a feeler gauge found I had up to a .018 gap in the cases right in the crank case area. Upon closer inspection, I've found that atleast one of these cases looked like it had suffered a pretty catastrophic crank disconnect and failure. The gasket edge was actually bent outwards, and wasn't sitting totally flat with its counter part. Plus there was a spot I knew that had a crack in it. Remember, these were junk cases when I started and I knew that
I've preached this in the past, but it is absolutely imperative that a motor have a good seal in the crankcase, cylinder, head, exhaust,intake, etc. If you can't pass a leak down test you are GIVING away HP and you will endlessly chase your tail for fueling and electrical issues when it is infact an airleak of some sort. I have a stock 250R motor with bolt ons only that embarrassed quite a few "built" 250Rs. But I had it where it would hold 12psi over night. So I am making sure that I am able to get the best performance possible out of this build while everything is apart and loose. If it doesn't run right, I want to eliminate as many variables as possible obviously.
I ended up surfacing each side of the cases on some sand paper taped to a piece of glass and found where my bad spots were. I just went over the whole gasket surface with a black magic marker and then sanded till it was gone pretty much everywhere else, to determine my spots.
Attachment 184289Attachment 184290Attachment 184291
As you can see in the pictures, the edge just wasnt sitting flat. I ended up working on this a bit more and got it really close, and then I ended up welding and building up 2 other areas (No finished picture yet, I'll get some). Working on these case edges had intimidated me a lot, but ended up being easier than I had thought it was. Rules being: Cleanliness is godliness on aluminum, pre-heat the entire work piece with a torch, and use appropriate sized filler rod. I ended up dressing these areas back out with a couple different stages of filing and my cases now seal within .003
without a gasket when bolted together

Cometic center case gasket is .020 thick.
As they sit right now, I've assembled the bottom end with the crank, main bearings, and seals. Installed the topend with the base gaskets, spacer plate, the head with its o-rings. Intake, and exhaust flange both installed. The only things I need is a rubber intake boot, a couple 5mm odd ball sized bolts for the intake, and the dang right side crank seal collar which is actually discontinued from Honda. When I get that put together I'll get to leakdown test the whole she-bang finally.