You should spend the money on Ford phasers.

Have you tried resetting the PCM by disconnecting both battery cables, using a jumper to each cable, hooking it all back up, then starting the truck and letting it run for 20 minutes? Not saying this will fix it, but has been known to correct some drivability issues.

 

I was going to get the Ford phasers or the melling phasers, but I cross referenced the Ford part numbers and the standard parts replaced the updated for phasers.

And honestly, I didn't even know about resetting the PCM. I will give that a shot tomorrow.

 

Spring for a Motorcraft coil on cylinder 6. Off brands don't have the best track record.

What brand of VCTs did you install? Again if not Motorcraft, possibly may be why you're beginning to get P0340.

I'd recommend not installing the Standard phasers. Read far too many posts of early failure of non-Motorcraft phasers and having to do the job over. Dive into a timing job and you'll understand why you'll only want to do it once - and do it right.

Can your tuner give you O2 data? Would be a good first step into operation of your cats. Sensor 1 on bank 1 and 2 should graph like a slow sine wave and sensor 2 on both banks should pretty much flat line. If sensor 2 mirrors sensor 1 on either of the banks, you may have a plugged cat on that side. This of course after engine is warmed up.

Lastly, you've already done a PCM reset. I referenced the procedure in your other thread. Won't hurt to do it again though.

 

My understanding is, if you can't use genuine Ford/OEM parts on these timing/phaser jobs, don't do the job til you can.