I was thinking possible bad BOV or diaphragm. Or could be possible bad VCT solenoids on that one side. Did you check you engine harness on that side for rubbing? I'm just throwing stuff against the wall to see if it sticks.
It started with the#6 misfire, so I moved #6 coil to #4 and it seemed at the time to follow, I purchased two new coils,(I've been down this road before) and the NGK Ruthenium plugs that I've read about on here.
I gapped the new plugs and changed those out along with the #4 coil.
I the start to get misfires in #6 again, so I changed out that coil as well. At this point I've been fitting this in when I make it home from being away for work, so I break down and take it to the local, to where I'm working, Ford Stealership.
I drop the truck off with complaints of #4 & 6 misfire and to check out the turbo on that side (on the way there I could hear a light rubbing/scraping noise coming from that side , with light acceleration.)
When I did get a call from the SA, the first thing he talks about is the very light dragging noise coming from the starter ( I have heard this occasionally, very Un concerning, not worried about it what so ever) and that it is in stock and they would be able to install the starter for $1100, WTF over.
I had to ask about the problems that it was brought in for.
"Well, you have NGK plugs in there, these engines will misfire if not the OEM plugs"
Fine, install OEM plugs. They get back to me saying that the turbo is fine, but, there is scoring on the #6 cylinder wall from what it probably a broken ring and letting oil in and causing misfire.
The engine could be rebuilt, but, might as well replace it for the price for $15K
Through talking with people I know in the area, the truck is now at a highly recommended independent repair shop.
On my way to that shop is when I got the turbo boost bank A code.
It should be looked at today, so, we'll see what they come up with.
I hope that this explanation wasn't too long and drawn out for you