I wanted to update this thread to leave some information for folks to find in the future.
Here's more or less where this bike is now:
It's a blast to ride and is rather well sorted out. For the sake of documenting, here's what I'm still playing with:
1. Carb flooding. I get gas flooding not just out of the overflow tubes, but even out the intakes. Appears to happen running or not running. This will fill up the airbox with gas when I had the airbox on, and when I'm running velocity stacks, it just pours out of them. It's usually the lowest (left) carb, but not always. It only happens occasionally. The overflows (tube and hose) are clear. The carbs are very clean and sorted through. The petcock works. The floats are buoyant, are set to the correct height, and the valves definitely stop the gas. The float pins are smooth and clean, and there's no sign of hangup or snagging. I've tested this with the bowls off in several different ways (shutting the floats manually, letting the rack sit in a tray and letting the tray of gas fill up and shut the valves, etc). When testing the rack on the bench, I get occasionally overflow out of the tubes, but never out of the intakes. Only happens occasionally on the bike. When it starts to flood and I can see wet gas sprayed on the side covers coming back out of the stacks, I start shutting the petcock manually to keep riding. Obviously this isn't a good solution. I have a few filthy racks of carbs, I'm thinking about entirely building a new set of carbs and swapping out.
2. Oil leaking. Largest leak is a light leak out of the end valve cover covers, which are 0-ring sealed. I've tried different size o rings, hondabond, etc. There's also a little oil seepage around various areas of the valve cover gasket and the tappet covers. The most annoying is a light oil leak out of the left (low) side of head gasket. This is especially frustrating because I had both the cylinders and the head surfaced and have gone through a couple of head gaskets now trying to get rid of the HG oil leak. Maybe it's just low quality gasket kits. I'm tempted to mill a dowel + o-ring recess into the head/cylinders like I've read about on other threads.
3. Goddamn rear wheel/spokes. I rebuilt the front wheel with a new DID rim, polished hub, new bearings, new spokes, and I've been trying to do the same for the rear. The problem I've hit is that it appears that the 77 on rear 550 hub is different than earlier models, and I've gone through a couple hundred dollars of spokes finding this out. The hub itself is a larger diameter, requiring shorter spokes by a few mm, and the spoke flange is much thicker, requiring a longer bent section on the outer spokes. If you try to use early 550 outer spokes on a late model 550 hub, you cannot bend the outer spokes around the hub to the center of the rim. Since it seems to be hard to find late model hub specific spokes, I cannot be the only person with this problem, but I've found little info searching the forum. For posterity, the flange is about 10mm, which is thicker by about a mm than the hub on the 750 we have here in the shop.The first set of spokes I ordered were just 'cb550' spokes, and I didn't realize that there were two generations of rear hubs. The second set of spokes I ordered (thai/japan ebay) were explicitly labeled 77-78 cb550f spokes, but appear to be identical to the first set. Looking at CMSNL, here are the rear hub parts numbers/generations:
cb550K
cb550k0 (1974) 42601323030
cb550k1 42601323030
cb550k2 42601323030
cb550k3 42601404000
cb550k4 (1978) 42601404000
cb550F
1976 cb550f2 42601323030
1977 cb550f3 42601404000
So, since I have a '77 and my hub is clearly different than examples of the earlier style that I see day to day (wider, larger diameter, different spacers, ribbed reinforcement of drum plate/stay brace), I'm assuming I have the 42601404000 version that's proper to my bike, and that all the spokes I have bought are for the earlier 42601323030 hub. I could order a proper set of rear spokes from buchanans, but I've decided that I can use these spokes I've already paid for by notching a channel for the outer spokes a few mm into the hub where the spokes wrap around the outside of the hub flange.
As for jetting, if I recall correctly, I'm running 110 mains and stock pilots and needle, idle screws set max lean, with stock everything except velocity stacks and mac muffler. Bike starts well, powerband is even and strong across, plugs look great. It only needs a moment of choke, and then likes to have the choke backed off, and I have to screw the idle stop in a bit to keep idle going while it warms, and then slowly back the idle screw down as I ride and the motor really heats up. If I'm correct, I think idle is still a bit rich judging by this behavior.. right? Either way, I will likely go back to the stock airbox from the current stacks and modify the mac muffler. I have to say that I'm baffled that it's acting rich at idle with stock idle jets, leaned out screws, and open stacks, and my only theory there is that the mac is causing so little scavenging that it's creating a rich condition.
Very little left to do. I can't believe how much work I've put into this bike - really soaking a lot of time into the details (clean hardware, cleaned up wiring, etc) has made it very ridable and trustworthy. It's fast, it's fun to lean over, and I like how it looks. Happy with this project as it nears the end.