2007 3.6 FSI VR6 Touareg idle normal?

I have been playing with this 2007 Touareg 3.6 V6 since January and it's slowly getting better. When I first got the vehicle it was limp mode, oil pressure flashing, and heavily misfiring. It is now driving kinda normal with no oil pressure warnings flashing.

I just finished repairing the PCV diaphragm, installed a catch can, sealed the intake manifold with liquid rubber, ultrasonically cleaned all the injectors as well as new seals installed, all new spark plugs, new coil packs, new fuel filter, oil change, air filter and new battery.

I sprayed quite a bit of Sea Foam directly into the combustion chambers when I had the intake manifold off and tonight was the first time I had everything assembled and started the engine for the first time after all that work.

She does idle better but she's still misfiring in cylinder 3, 5 and 6. The high pressure fuel pump sounds really loud to me and the automatic transmission is now having issues finding the right gear.

I guess it's time to change the fuel pump and get the transmission serviced at least.