The rev limiters I know are electronic things that connect to the ignition and I wasn't aware of any two strokes that had them.
I am also confused about what it is you took apart to clean. I would take a carburetor apart to clean it, the airbox apart to get the air cleaner out to clean it, but I wouldn't disassemble any of the engine just for the purpose of cleaning.
If for some reason you took off the clutch cover then you might be having trouble getting the water pump and or governor back into their respective spots. I had a similar problem on my YZ-125 recently when I changed the clutch. My mistake was that I put the governor in upside down. It was pretty obvious one I stopped and took a close look as the gear on the governor needs to be out (away from the cover).
If that is not it then you are going to need to give us a few more details as to exactly what you took apart.
Rod