What's the proper break-in procedure for a Yz 125 with a new top end?

If you ask 10 mechanics, you will get 10 different answers.

I have broken in hundreds of bikes and have used and tried a dozen different methods. I have broke in bikes by just letting them idle, I have broke in bikes by just riding them slowly and i have broke in bikes by letting them get to operating temp and then riding them hard. I custom fit my rings on my race bikes, so break in is extremely important. If you are just purchasing the rings off the shelf and not custom fitting them, it is not as important because the tolerances are much greater with the standard off the shelf rings.

What have I found to be the best? Idle break in for AIR cooled bikes. Operating temp and slow 15 minute ride for water cooled bikes.

Your 1998 is a water cooled bike. So I would use the operating temp, 15 min ride. It works like this. Start the bike up and let it idle for about 8 minutes. This warms up the engine and water. Then take the bike out and ride it for 15 minutes. DO NOT hold the throttle wide open this first time out. After you ride for 15 minutes, let the bike cool down so that you can touch it. Repeat, but this time after you have ridden the bike for approximately 5 minutes, hold it wide open through a couple of gears, then tone it back down for the remainder of the ride, stop and let it cool down to the touch. You are now done breaking in the bike after it cools.

Remember to always let a water cooled bike warm up for a couple of minutes before you take off.

I have to agree with IanK, except you do need to feed it a good bit of throttle to seat the ring.

Soooo....short bursts of 3/4 throttle followed by a "downrun" of twice as long as you stayed on the throttle. Don't load or bog the engine down. Don't scream it, but don't be afraid of moderate revs for the first few minutes.

Just take it easy for the first few hours, like an easy trail ride with a little bit of higher RPM for short bursts.

Best to do the first session for no more than 15-20 minutes and stop and relax for about the same time.

1 heat cycle (till radiator hot). No constant or hard throttle.

Retorque.

Warm up, ride easy till hot.

If sounds good. Hammer it, done.

Assuming you prelubed with a little premix oil on walls, wrist pins, etc.

No use spending hours breaking in a 2 stroke motor, especially if it has a 20 hour top end lifespan (if you ride hard).

i'd use alittle extra oil in the gas for the first couple of tanks, run it easy and stop and let it cool off after 10 minutes or so .. do that several times gradually extending the intervals .. i personally wouldnt run it wide open in the power band until after i ran the first couple of rich tanks through it either, then after i did reach that point and open it up real good i'd stop and let it cool off again a couple of times .. of course change the oil .. you may need a new plug after the rich tanks ..