break in help

well I finally got my bike running(92 Yamaha wr200), Long story short, I rebuilt the engine, screwed up and had to get cylinder re-sleeved and buy new piston, I also had to replace power valve assembly(turns out it has never worked). I then rebuilt it the right way and put it back together. All that took 2 months!

I just took it out for the first time. I ran it for about 8-10 minutes, no higher than 3rd gear and low RPM. I am letting it cool down and will take it out again for 8-10 minutes but push it a little harder in higher gears. then repeat with bursts of full throttle. Then according to the manual I'm done.
Is there anything else I should be doing.

I am running "Gold Spectra"(think that's what it's called) oil (52:1) with 93 octane fuel(the man who re sleeved the engine said to do this). The only mods to this bike are UNI air filter and boyesen power reeds(both installed during rebuild, first time running with them). I leaned out pilot screw just enough so it runs and doesn't smoke a lot.

When i was running the engine seemed a little rough(improved slightly by end of run), is this normal for break in?

Please respond.
Thanks!

Update

I just took it out for a second ride. I adjusted the pilot screw a little and it ran better. I took it out and ran like last time for 5 minutes and then planned on riding harder just like the book said. After I had been putting around in 3rd for a few minutes the bike started loosing power and stopped. I immediately killed it thinking a piston clip came out and ruined it again. I started rolling back home(it was down hill here.) When i got to more of and up hill I turned it back on and it worked fine, I then opened it up in higher gears and it did great. Another problem is at idle and slow speeds the engine seems to give pulses of more power every few seconds. I'm assuming it is just idling high but i though I would ask here.

well I added more oil so it's now about 25:1
I took it out again and it ran awful. It sounded sorta like a wind up toy. It got worse as i went so I slowly rode back home. By the time I was home it would barely stay idling. When the motor cools I will pull the plug and check it. I will try messing with the pilot screw some more. The bike also has hardly any low end, really struggles to get off the line and in acceleration(if that helps diognose the problem) please help!
Thanks!

thanks. I meant I was riding it for about 8-10 minutes each cycle, I let it cool as long as it takes for it to be cool.