Not to be funny, but I think I would have warmed it up good and did a good compression test dry and wet early on to rule out valves seating poorly. Just to have that info for sure. Any time I hear poor pulses and lack of smoothness till higher rpm’s I always want to know what the cylinders are capable of before I get into spark, timing etc. Even crappy valve seats from setting will cause some symptoms like you first described. Good pick up on the timing issues.
I hope you got all the bugs out.