I just finished same thing on mine this weekend, but kept stock bore.
Every engine i have ever built, which have been alot of truck/machinery/boats/etc.
I have started them, ran the rpms up to high idle, and held there for few minutes. shut down, look over engine. restart and ride/drive/run it hard as you please. never a problem. all this do this break in and this and that sounds alot like letting the motor get part way worn out. if all the clearances are right, and you built it right, just get on and ride.
the only exception to this, was when I was a repair facility for Ural motorcycles. those the machine work was poor quality at the time, and they needed break in, the first thre oil changes the oil would glisten in the sunlight with the metal particles floating in it. both engine and trans.