One last check, pressure check the carbies, and install a clear pc of tubing on the fuel return line, and look for bubbles. Also, a clogged vent will do just about what you describe. Runs great, until vacuum develops in tank. Loosen the gas cap (Don't loose it!) and see if you hear a FFFFF. IF you doo, well you have it.
Another stunt you can doo to see if it is fuel related, is to:
Take a full can of silicone spray, and duct tape it to the side of the doo. Within hands reach, with the left hand. Run a temporary tube down to the top of the spark arrestor screen, at the fogging hole. Now, next time she shuts down on you, reach down, and hit the spray of silicone. IF it improves, THEN you know it is fuel. IF it does not improve, then you know it is electrical. Timmy Boy has a method to check the electrical with a jumper. Also, there are little plugs you can place on TOP of the spark plugs, that have lights in them. When the plug fires, it lights up. Now, if you can run it with the seat off, nxt time she messes up, you can SEE the plugs and SEE if they are getting spark. At some point you have to corner the problem. Maybe even a trimming of the end of the spark plug wire, (trim 1/4") and re-install the boot, that goes on top of the plug.
Sometimes FINDING the problem is harder than FIXING the problem!
My philosophy is that if it was built, and designed by a man, then a man can FIX it!
Nate