86 Trx 350. New motor not running right. High idle when warm.

Quick overview; I acquired these Atv’s both with seized motors. One has a trashed piston/cylinder/crank and the other had a trashed bottom end. I put a new cylinder/piston on a bottom end I had laying around and put it back in the bike. (I haven’t started in on the motor with the trash lower end yet. Still waiting on parts for that motor).

Ok so I got my zombie motor all put back together and installed in the bike. I flushed the motor with diesel since the lower end had been sitting open in my basement for a few years. I filled it up through the dip stick hole and with the spark plug out I cranked it over for a few minutes, drained through a cheese cloth and poured it back into the motor. Lots of chunks and even some very fine metal shavings came out. I did that 3 times, then filled it up with cheap oil and put the spark plug back in. She fired right up without a complaint and idled nice for about 10 minutes until I shut it down and drained the oil, put in a new filter and refilled with oil. Thinking everything was great, I installed the intake box and tubes to complete the intake system. I fired it back up and after a few minutes of idling, the rpm started to climb.

I believe its an air leak, since it was a pain in the ass to get all the intake tubes hooked up and before they were hooked up it ran normal. Also because when it starts to idle high, I can pull the choke and then it runs like normal. But, the idle screw on the carburetor is hard to turn and doesn’t seem to have any affect on idle speed. With the choke on everything sounds and looks good. Great throttle response and produces good power. Starts on first crank every time. I inspected the carb boot and it looks good. All clamps are tight.

I noticed that on the bottom of the carb there are 2 nipples. one looks like a drain for the float bowl, and the other is right behind the idle screw. Is that suppose to be plugged? There are breather/vacuum lines, but I can’t see where it would plug into the carb. What should my next course of action be? Should I do a starting fluid test by spraying the fittings during idle? Also, I know that the crank case isn’t sealed completely, although it doesn’t leak oil. when I filled the crank case with diesel, it was leaking pretty good from around the output shaft, but I wouldn’t think that leaky crank case would cause a lean condition on a 4 stroke. And i thought lean conditions made for difficult starting once warm. When its cold it seems to idle fine for maybe a minute, then like somebody is playing with the throttle the rpm starts climbing once it starts warming up. Any suggestions?