I am from the camp that thinks if something ran correctly BEFORE I worked on it, then it was something I did (or failed to do) that's caused the problem. I personally would rule out failed parts as the problem and get an accurate set of vital signs of your motor. Compression (the third thing a motor needs to run) for baseline information, spark (verify that you're getting equal visual spark to each plug), timing (rule out firing order mistakes).
A thorough carb cleaning is complicated but not beyond the capabilities of average mechanical aptitude, if one is observant for the details. Same goes for the R & R process.
Did you drill out the pilot screw access plugs and remove the pilot screws during your cleaning operation? If you didn't open up all of the carb's passageways and blast them out with cleaner, then you can be sure they're clean. After verifying that nothing was missed in the electrical department, like an unplugged wire to a coil, for instance, then I'd concentrate on a thorough fuel system service.