Hi, KL! Happy to assist. Yes, please bench break in. It'll likely help a lot.

Given the same problems with two new engines in the same setup, I'd really take a look at the muffler. If the backpressure isn't enough, that'd explain the erratic running. Again see if you can find a way to use the stock exhaust, even if only for a test run on the ground, to rule that possible problem out.