Runs great for a short ride....then won't start!!

when i first got my 550 it was doing something similar to what your bike is doing, new battery and good carb cleaning took care of it.

 

If you can pop start it that would point to the starter. Try that first.

If you can't, you need to eliminate the fuel, air, spark, and compression. That should be easy to do, in fact, fuel and air problems don't just start happening suddenly, engine temperature variations don't affect the carburetor directly, so if you can have it running, turn it off and it immediately fails to start, then it is almost certainly spark or compression.

Check your valve clearances. If they are too tight you may not have enough compression for starting. They get tighter as they warm up. I still can't imagine how it would run right before, but won't hurt to check.
Check your compression before a ride, and then after, when it won't start. Do both wet and dry tests (google it). That is unorthodox, but if it changes SIGNIFICANTLY, that might narrow it down. What I'm looking for here is hard to explain, so do a lot of research on what you are looking for in compression tests first. It is variation between cylinders, not variation between tests, that will provide you with information.
Also, check your plugs right after you shut it down. If it is black or very white, or anything but the proper color, that might indicate the problem.

Do you have new plugs? What type are your plugs? If you don't know or can't tell, get new plugs. In fact, you are running new, correct plugs, right?
Have you checked your coils for the proper resistances?
You answered almost all of fitz's questions except the one about the fusebox, check the resistances across that.
Check your alternator output, also. You can see how to do these things in Chacal's catalog, Pg. 2. With one addition, check the resistance of the caps and wires together, IN ADDITION TO them apart. That will determine if you have a bad connection from the wires to the caps.
If those all check out...CAREFULLY go through the connections in the headlight, and under the left panel. Pull them, clean them, grease the connector with dielectric grease (read up on how to use dielectric grease first), and reinsert them. In fact, if it were me, I'd clean one connection, test the bike, then if that didn't fix it, keep going. Start under the left panel. That's where the ignition controller is. If you feel like tracing out the relevant connections from the manual, fine, but it would probably be quicker just to do them all.

And one more thing, since you say it will start no matter what the choke is, try starting with the throttle open in varying degrees. Maybe it's too rich, if your butterflies are too far closed, then it may be too rich to start when warm, but it would lean out (why you need choke) when cold.

You don't have to do everything in that order, I just kind of threw it together. Do the easier tests first. That's all I can think of for now. See you in a month!! 8O