Low compression on one cylinder?????

Check the choke plate on the carburetor for the bad cylinder. There should be a spring loaded flap covering the D shaped opening. If it's missing, chances are that the flap, or actually a tiny sliver of the flap) was holding the valve open slightly, but messing with it made it come loose, so all is good now.

Several 550 riders have reported this over the years, but they never had to take the motor apart. Once the piece came loose, they got it out with a magnet, and the bike ran fine after that.

Strangely, the flap usually makes it completely through the motor with no remnants.

However, a propr leak down test, as the other guys mentioned, would have showed the problem, so maybe it was something else. If you heard no air leak during the leak down test, though, then where was the compression leaking from?

The carbs were off the bike when I did the compression test. I did not hear air coming from anywhere but I don't hear that great anyway

I think tomorrow I will take the head to my local bike shop and have them remove the valves. I have a valve spring removal/installer for a car but it won't work (too big). I need to find my valve tray or I'll use a shoebox, poke some holes in it, and number them.

You could always make your own tool with a c clamp and a socket
homemade valve spring compressor
You will also want some compound to clean the valve seats:

Here's my plan, if it works, it works. If not that'll suck. I downloaded a PDF of the manual last night. It gave me all the specs. If everything checks out, I'm going to lap the valves and put in new seals, clean up the piston tops and ring grooves and put it back together. I'm going to put a straight edge across the head also to check for warpage. I ordered a full gasket set cause just buying the top end gaskets were almost as much as a full set plus I got valve seals.

Lots of folk go ahead and install new rings while they are in there. Dealer's choice, obviously.

Probally should pull the pan and clean everything out too. The oil pan is gonna be a mess.I used a little gas then wd-40 and 3 big cans of brake cleaner. Kerosene would be better than the gas but if your very careful. you should be ok.

You'll be surprised just how nice you can get the trans, crank and internals without splitting the case. My oil pump needed a new screen too and to be all cleaned out. had 4 or 5 tiny sharp pieces of steel sticking in it for some reason.

Thinking the new rings idea and a hone job would be a very good idea too since you have it this far.

Kerosene would be far better. I stopped using gasoline as a cleaner ages ago.

I had the valves removed today. The intake valve on the low compression cylinder had oily carbon deposits built up big on the underside of the valve. I noticed a thin line wore into the angled section of that valve. All the others were good. May replace that valve. I took my coils in to have them tested on their machine and both had very long cracks in them. MONEY PIT :ohmy:

Here's a pic of the valve. The one on the right has a groove worn into it compared to the left one. Should I replace it or just lap it in?

Depends on how deep it is. Personally, I would try to lap it in.

It seems deep cause it catches my fingernail