About to pull my hair out...Any ideas?
 

First post, sorry if it's in the wrong place and that it's so long.

So I was towing my boat and got the flashing check engine light and misfire. Went and got the codes and it was lean in bank one and misfire in cylinder 3 (p0171, p0203, p0303). I changed the fuel injector, plug, and coil on cylinder 3 and noticed a vacuum hose was bad and replaced that. I also replaced the MAS. The check engine light is now off and doesn't flash, but the truck seems to misfire when in idle and under a load (slowly accelerating from 60+mph). I used the cab cleaner method to look for leaks, but didn't find any. I hooked up a pressure gauge to the passenger side vacuum tube and at idle it's 14" Hg. When revving to 3k rpm it dropped to 13" Hg. I then tested the vacuum at the air intake on the driver's side and it read 22.5" Hg at idle. So, I thought it might be a plugged cat converter or exhaust. I took the cat converters off and upon startup it was still idling rough intermittently. I also replaced the fuel filter and it seems fuel pressure if fine, but the stupid kit I got doesn't have an adapter to fit the fuel line that goes into the rail.

Where do I go next?
PCM?
DPFE sensor?
Head gasket?
Stuck valve?
Compression test?
Short in wiring harness? Where do I check?
Could other coils going bad cause the issue to persist even though no code is showing?

I prefer fixing myself, and usually do my own work, but I'm getting so frustrated chasing the issue. Still, there is no check engine light, so I can't tell if any codes were cleared or if there are new ones.

Any help is greatly appreciated.

Oh yeah...2006 5.4 4x4

Mileage? Last tune-up ?

135k mi. Oil change 2k ago. Plugs and coils 1.5 years ago (15k mi)

My gut says compression test to rule out valvetrain and internal before throwing any more money at it

Do you have an Android phone or tablet? If so you can use it to very easily tell if there is actually a misfire.

homemade smoke machine on you tube
 

for more testing of vacuum circuit , I made mine out of a 1 gallon new paint can,duct tape,schrader valve . some fittings and a pack of cheap cigarelos-- pump a little air pressure in can into brake hose fitting with clear tygon to see flow of smoke . My leak was a defective purge solenoid . Took me three burns to get it done .
I would look at number 3 injector plug ,clean it and see if signal getting there .Scope would be nice or volt meter .
Did you clean snout area of sparkplug in cyl with carb cleaner . carbon build up causes problems . Can break new plug .
Did you use new boots and dielectric grease .
Any chance that when you disturbed orings on fuel injectors lifting rail that they are dirty or sucking air , usually use engine oil on rings after cleaning holes .

Yes. How?

Yes I used new boots and springs. I vacuumed out the plug hole before and after removing the plug, but didn't spray any carb cleaner in it. I might have a bad seal on the injectors, but no change in rpm when spraying each with carb cleaner while running