Hey SS6, thought about a couple things with your setup.
1. That's a huge change in main jetting. Be prepared to pucker when you take it up to highway speeds!
better yet, be prepared for the engine to rev and die. Make sure you have some room to coast to a lower speed and then it will catch and/or put it N and restart.
2. Get some collectors on the exhaust and the combustion should clean up. Carburation may appear to change as well.
Idealy A length of around 22" from the ends of the primaries, or a multiple, like 44. Atmosphere is shoving hot exhaust back into the cylinders. Don't be surprised if you see exhaust residue in the intake. If its all the way up to the plenum, that's not good.
Have fun learning