I think your problem is with your carburetor. The fact that it starts probably means that your valve springs are O K. Valve lash as well. Are you running the stock muffler, or do you have a header pipe exhaust? I have built 301 on one of my karts ( rod, flywweel, cam, milled and ported head, 50 lb springs, header pipe and intake ) . I run the stock carburetor with a #40 main jet and the pilot jet drilled out to .021". With a 40 series converter with the light weights and stronger springs it surprises me how strong it leaps out of the hole and get to the upper 40's real quick. I am not a big fan of the Mikuni's, and don't know a lot about them. When you did the mods to the engine did you do everything at once.
Did it run properly before the mods? Are you getting good fuel flow. The fuel intake port on the Makuni could be higher than the stock carburetor. The gravity flow to the stock carburetor while adequate doesn't leave much room for being altered. Do you still have the stock carburetor. If so, try jetting it as mentioned above. With what you have done it won't good with the stock jets, but the #40 will only cost you $ 3.50. Wish I could be more help on your Makuni, but I don't think it would be starting and running for a short while if it were valve or timing related. How does the spark plug look. Is it black and sooty, or does it look too clean.