Great Job!
Your engine/brake/tank story was Exactly like my 350F, except for the crankshaft seal and spark advance unit. My bike had set for many years neglected and un-ridden. Thankfully it was kept in a garage, out of the sun.
Mine came with a Martek440 electronic ignition, instead of the stock points set-up. It also came with newly mounted rim strips, tubes and cheng shing tires, plus a new chain. So I didn't have to deal with that.
It sounds like you went through all the recommended service items, and she fires up. Does it idle?
Make sure you remember to set all the air-screws on the 4 carb bodies to 7/8 turns out from lightly seated. You can adjust them up to (+/-) 3/8 turns, but I would do a carb synch before moving them from 7/8.
If you can get it to idle, which it sounds like you can, set the cam chain tensioner according to the manual. Then sych the carbs, dial in the idle adjustment to 1200RPMs, and you should be good to go.
Make sure you really bleed all the air out of the front brake system. Sometimes after sitting a while after a rebuild, all the tiny air bubbles collect and you can bleed it out again. Check for a hard lever feel.
At first, my bike got poor mileage, and was fouling plugs. Around 28-32 mpg. If your air filter looks grey or grimy, replace it with a fresh new white one. It made a world of difference in how the bike breathes, and now I get 42+ mpg and the bike performs amazingly. At this point I am ready to fiddle with the air screws and find the sweet spot.
Good luck and keep us posted!
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Also, add yourself to the list (which I need to update)
HERE:
http://www.sohc4.us/forums/index.php?topic=23960.0