3.4L Back fires and I need help

I need some 3.4l experts advice/wisdom

My 01 Taco 4x4 3.4 manual runs like sh*t. It idles fine, but backfires, misses and Boggs down above 2,000 rpms only underload(revs all the way up to 5k in nutreural fine)
It backfires from the intake not the exhaust which points to the engine running lean
So here's what I've done so far:
-Checked for vacuum leaks (there are none that I can find)
-replace fuel filter
-replace intake gaskets
-replace spark plugs/wires
-replace all ignition coils
- replace maf sensor, throttle position sensor, o2 sensor(upstream)
-replaced fuel pump
-replaced all fuel injectors
- checked valve timing (all timmimg components were replaced 2,000 miles ago along with water pump and thermostat.
-cleaned throttle body

All of these items have done nothing! And I am completely stumped.

--Also a side note, I recently replaced the engine with one out of a 99 4 runner, but it has ran really good up until last weekend.

 

@mechanicjon
@Glamisman

Did you ever check the fuel pressure when swapping out parts?

 

Yes, fuel pressure is good

 

Plugged cat maybe? Try lessening the exhaust pipe from manifold. enough to allow about 1/4 inch gap. Then test drive.

 

When did this start running bad? was it gradual or all of a sudden?

 

I've heard that using the wrong spark plug could have issues.

 

+1 for correct plug usage. 5VZ-FE requires dual grounded plugs.

 

I'm using dual grounded denso plugs

Both cats are completely gutted because they were clogged about 15,000 miles ago and I didn't have time or money to replace them at the time.

The problem started last weekend and got worse as I drove it.

 

Ouch, your secondary o2 must be reading some fucked up shit.

 

I just get a cat inefficiency code, but it has never affected the proformance of the engine.

 

I would make sure you have no exhaust leaks.

 

I have one small exhaust leak in the muffler

 

@Speedytech7

Any help?

 

@AK1stGen
How’s the head gaskets? There’s a few ways to test...

 

I've done a compression check and there's no oil in the coolant and no coolant in the oil. So that rules out head gasket. Compression was between 170 and 175.

 

after all of the parts replaced the only thing I can think of off the top of my head is the fuel pressure regulator... pull the vacuum line and see if there is gas coming out of it or in the line.

 

I'll check the regulaator, so when I pull the vacume line off gas should be coming out the return line? Is this with the engine off? I'm little confused with what you meant by that

 

Do you think the ethanol has contaminated the tank? Condensation & water...here’s a good article from Popular Mechanics:
http://www.popularmechanics.com/cars/hybrid-electric/a6244/e15-gasoline-damage-engine/

 

How is your catalytic converter? If you hold it up to the sun can you see through it?

 

He said they're gutted I believe?