Yoy need to jet for the new pipe, you will need to be considerbly richer.
The reason for reduced smoke is probably you are running too lean.
What carb is it you are running. I am only familiar with Mikuni carbs and I would start with a #270 - #280 main ,needle on the middle clip, and do plug chops until you get it right.
lol danm that seems like alot. pretty costly repairs. when i got my jug ported they honed the cyliner and said everything was fine bc i wanna get the most out of my topend. how long have you been riding?
idk the pilot size in the carb bc i couldnt find it anywhere but the main jet is a 155. is that stock in a keihin 35mm carb??