Stopping the knock: Lower compression and ported heads...

...It feels a bit rougher at idle and the idle vacuum is certainly lower...

Ports are bigger in volume, and compression is lower...these are the manifestations of those input conditions.

I may need more initial timing.

...probably...but you didn't quantify your initial since reassembly either. Did you recurve your dizzy yet to limit your total advance?

I'll probably need to go with smaller jets since I'm running in the 12.0 to 12.8 range

Time to drive with a friend and map it.

Power feels pretty good but the secondaries don't seem to be opening fully. It doesn't seem as loud at WOT as before.

Quite likely all related...

It feels a bit rougher at idle and the idle vacuum is certainly lower. I may need more initial timing. I'll probably need to go with smaller jets

...time to start back to square 1; minus your detonation...hopefully.