Sorry to hear you're off the road.
Was there a reason you got rid of the cone and have the bigger air filter on the bike now?
When I had the head reworked for better flow (just better all around than the factory head) by Ace in 2014 I also went with the Ace air box. It provides a plenum; a quiet, undisturbed, safe place for the air to sit and wait to be sucked in rather than a cone out in the airstream. After the headwork, the TM32, the exhaust improvements, the Pertronix, the engine just performed all around better; quicker easier revving, smoother, quicker to a given speed in any gear. Just all around way better than stock. It went faster in 4th than I ever really cared to go & 5th was just loafing along at 60.
I have the flowbench charts, but my feelings on on-the-road performance are all seat of the pants. It was just an overall better engine. Oh yeah & the switch to Champions over the NGKs was a vast improvement I really can't explain except for the fact that they stayed cleaner. I tried 2, 3 & 4 heat range. I think I settled on 4.
There's a lot written about all this & tuning & improving the AVL back in the dusty stacks. Back in 2012, 13, 14 & forward. And a lot of the ironhead stuff back then also applies.
My biggest mistake back then was not having Ace install an ironhead decompressor in the head when he did all the other work.