Heat cycling wont break-in bearings. Rolling element bearings don't break in, anyways. Rolling element bearings shouldn't wear at all within their lifetime (ideally, rolling element bearings fail due to fatigue, spalling, and not wear). If the bike is rebuilt, the cylinder has already been thoroughly stress relieved through heat cycling. The only reason I can think of for letting it cool off is that there is more friction between the rings and cylinder. I say start it and run it light for a bit. Then, shut it down for 15-30 minutes to let everything cool. Start it up and cruise around a bit, run it just hard enough to keep it clear. Then, you're good to go.