2006 Possible timing issues
 

Okay, I changed the number 4 and 5 coils. About 2hrs later the truck started stalling and pinging when at idle in gear. I had the P0022 code. So after research it appears as though I am having the dreaded timing issues. So I replaced both VCT's and it did not fix the problem, however if I unplug the VCT's the stalling issue goes away.So I need help figuring this out. What I dont understand is did I do something when I changed the coil or is it just coincidence?

You are giving us peace meal info.
Some questions that come up are, why did you change the 2 coils?
What engine is in the vehicle?
If you unplug components with the key on or engine running , you risk creating voltage spikes into the system and can wipe out the PCM.
Whatever is going on is affecting bank 2 and it could be mechanical or electrical at this point.

It is a 5.4L. The spark plugs went out and I had Ford change them, the coils stsrted to go out one by one due to the failed sparks plugs weakening them. Currently when I drive the vehicle I leave the VCT's unplugged.

There are a few things that could be giving you "heartburn".
Of course mileage can affect some of this, but the VVT system is dependent on clean engine oil circulating through the system. There could be a problem with the tensioner on that bank, a problem with the phaser on that bank, the chain may have jumped a tooth , an electrical problem to the solenoid to that bank and probably a few more items. It may be time to have a good capable scan tool check done to see what has changed .