Hello emilios!
Congratulations to your successfully rebuilt engine and good luck with it!
I will describe what I usually do for running an engine in. I'm sure other people will have a different approach, this is one of the topics that is well suited to start a LOOOOOONG discussion.
Ok, now what I do is run the engine on a larger main jet (next size) for the first 1000-2000km, to give it better internal cooling by richer mixture at full load. Then I ride it solo on plain areas without going uphill. I open the throttle not more than half way and cruise around at about 80km/h maximum. Some times it is advisable to open the throttle a bit further, maybe three quarters, and accelerate a bit, in order to prevent glazing of the cylinder walls. This is only done for a few seconds, then I slow down again to about 60 km/h and let the engine cool down. So I always try to ride the bike at different speeds, accelerating from time to time, but always keep the loads and revs down for the first 1000km. Then I slowly start to raise loads and revs during the first 3000km. Then I consider it to be run in completely and able to cope with some serious riding

HTH, Markus