Homer Simpson.....................a great guy and kinda my hero! We share a common bond, since we both worked in Nuclear Power Plants.
Actually, now that I think about it, we look alike as well
Back on topic...........................if you have solved the air leaks, then its time to focus on the carbs. If you have stock CV carbs, they are great carbs, that work really well. But, and its a big but..........................they are a precision device, and everything inside them has to be working correctly. Make sure the float levels are set correctly. Butterflys must be able to close 100% and synced to each other.
With your stock air boxes and stock exhaust, you should be using the stock size main and pilot jets, that 5twins has listed on his table about carbs. Have you remove them and confirmed they are the correct size? Yamaha engineers (likely with Mikuni's help) tested and installed the correct size jets, and they will work for you. Make sure the pilot jets are not partially plugged, as can easily happen, due to the orifice being so small.
If the above is correct, then you want to use the dead cylinder method, to adjust the mixture screws. I find it works best for me to get the rpm down low, to maybe 500 to 800 rpm while running on the one cylinder. Use a fan blowing air across the engine.
On my 1978 SE engine, using stock air box and stock exhausts.......................guess what..............the stock main and pilot jets work just fine. I had the mixture screws adjusted to 3 turns out, with the stock #27.5 pilot jet, and engine ran quite well. However when the mixture screws are out at 3 turns, they are so far open that they lose the throttling ability of the needle, and its more difficult to sense the sweet spot,when the perfect mixture is found. I replaced the #27.5 pilot jet with a #30 pilot jet, to see how that would work. I found my new sweet spot was at 1.75 turns out, and because the mixture needle was at a better position to throttle the mixture flow, the 1.75 turns was much easier to tune.The 1.75 turns was right on the money, and I've been using that setting for the last 5 years, and no longer ever touch them. That's how Mikuni CV carbs are........................once you get them set right, you just leave them alone.
With the 1977, you have a different version of the CV carb than I do, but the same principles apply. Just thought you might be glad to get benefit of my experience.