The info below was for a 2 stroke and included doing a plug chop and read so as to set correct mixture.
Also ensure correct fuel mixture is run and a decent brand of oil.
This is from CT Racing, I have found it works well!
RUNNING IN YOUR NEW MOTOR
CT Racing in the US has this proceedure listed on their website as a recomended running in proceedure for new engines or new piston/bored & honed top end. I followed this after I rebuilt my engine, it takes quite a while but these guys know what they're doing so if it saves you some grief in the long run it's worth in i'm my books.
http://www.ctracing.com/ Break In Procedures
1. Start your engine and let idle occasionally blipping the throttle for four to five minutes. Allow the engine to cool completely. Repeat this "heat cycle" process four more times.
2. Warm up the engine again and ride the bike for five to seven minutes at a very easy pace, vary the rpm, don’t ride at one speed. Don’t ride at more than 1/3 throttle or more than 1/3 rpm. Let the engine cool down completely and repeat the initial break in ride. Let the engine cool down.
3. Check the base nuts and head nuts for proper torque, check the coolant level and add coolant as necessary.
4. Ride the bike for five to ten minutes at a moderate pace, vary the rpm, don’t ride at more than 3/4 throttle or more than 3/4 rpm. Let the engine cool completely and repeat this secondary break in twice more.
5. Replace the spark plug with a new one. Ride the bike for five to eight minutes at a moderate pace, vary the rpm and shift up and down the gears. Once the engine is up to operating temperature you can make a jetting pass. Start in second gear and ride at full throttle through fourth gear, fully revving out fourth gear. With the throttle wide open in fourth hold the kill button down, pull in the clutch and stop. This is called a "plug chop"
6. Read the spark plug. With a pocket flashlight and a magnifying glass look at the porcelain part of the plug only, as you view the plug from the center electrode look down the length of the porcelain to its base, at this point there should be a dark chocolate colored smoke ring. There was not sufficient time to thoroughly color the whole plug, so the nose of the insulator may still be white, as long as there is a visible dark ring at the base everything is OK. Remember we want break in jetting so the plug should read rich/dark. Richen the jetting as necessary. If your having a hard time reading the spark plug, after the jet pass put the plug in a vice and hacksaw around the plug at the washer. Break the threads off with vise-grips, and the porcelain will be easy to read.
7. Complete the break in by riding at an aggressive pace for fifteen minutes, vary the rpm and don’t cruise at part throttle, ride hard without revving the engine too high. At the end of this final break in session do another jetting pass/plug chop as described above. Check the spark plug for the correct dark/rich condition. Wiseco Piston equipped engines will require another one or two break in cycles, ride at a recreational pace not revving the engine hard, full throttle should only be used for very short periods, fifth and sixth gear should only be used to cruise, ride one tank of gas through the engine in this manner to complete the break in. We feel it take about two gallons of gas to break in a motor equipped with a cast piston and five gallons for a motor equipped with a Wiseco.
8. Replace the spark plug with a new one, ride the bike aggressively for eight minutes and do a jetting pass/ plug chop in fifth gear. If the porcelain color is still dark/rich, lean the main jet size one at a time until the smoke ring at the base of the porcelain is a light brown. If the porcelain base is white, don’t run the engine and contact CT. If the plug color looks good, continue riding at a race pace for ten minutes. Stop and let the engine cool. Check the torque on the cylinder base and head nuts.
9. More on jetting. If you generally run your engine flat out in sixth gear then make your jet pass/ plug shop in sixth. Motocross jetting is checked in fifth gear, therefore it is not safe to run MX jetting in the desert or down a road wide open in top gear. Desert jetting is richer than MX jetting. When running an engine at full throttle for extended periods be sure to chop the throttle decisively to slow down, just rolling out a little can seize a well jetted engine.
CT racing 11805 E. Slauson Ave. Santa Fe Springs, Ca. 90670 ph. 562.945.2453 fx. 562.945.7006