Head Gasket Replaced Now Chasing Codes

Current P0301 Engine misfire

First a little background,

2012 Prius 2, replaced head gasket. During this repair, when reinstalling the timing chain the tensioner did not release so the chain skipped a couple links. I took everything apart again and set all retiming according to the Toyota Repair Manual. Everything is in time now.
After reassembling everything, I fired it up in maintenance mode. It cycled through rough idle as the air worked its way out of the cooling It displayed. It eventually displayed the Check Engine light. I read the code using my Techstream. The code was PO108. I cleaned the MAP sensor, also the intake manifold again and took it for a drive. There is a knock that speeds up and slows down with acceleration as the car is driven. It does not seem to be there as it is idling/running in park mode.

The only code that comes up now is P0301.

In addition to the head gasket, I have replaced
All sparkplugs
All ignition coils
Cleaned MAF and MAP
Cleaned EGR and EGR Cooler
Replaced PCV Valve
Replaced the timing chain tensioner.

Does the EVC for the engine need to reset/reacclimate due to the new head gasket?
Any advise is appreciated.