2003 SOHC 4.0 Rough idle, need help with diagnostic

Everything was going good a few weeks ago. Drove 30 miles away in no hurry. Topped off the tank on the way back bc gas was cheap. Started running rough immediately afterwards. Temp started dropping to the bottom of normal and bumping around there. Poured in a can of seafoam with fingers crossed. Nothing. Couldn't drive more that 2k rpm. Revved fine in neutral. I'd rev it and dump the clutch and get a little speed then lose power. Called my mechanic while limping down the highway. He was stumped and hesitantly mentioned water in gas. I got to an Advance and added some Heet. Immediately ran better. Got home but the temps never came back up. Ran that tank out and filled up with 89 just to help things along.

2 weeks later I made another decently long trip. Started running bad again just before I got home. CEL started flashing -- misfire. No codes were stored and I can't get it to blink again while plugged in to scanner. This time it hasn't run right again. Won't rev past 2k without bogging down, and sometimes cutting off. I can go about 10 mph in 4th gear but no power or torque. So here's where I started:

1. NGK plugs and wires
2. Swapped out used coil
3. Replaced fuel filter
4. Replaced CKP sensor
5. Swapped out used CMP sensor
6. Cleaned IAC with MAF cleaner
7. Cleaned MAF with MAF cleaner
8. Compression Test (162-178psi)
9. No milk in oil. Coolant bright green and
9. Faint smell of coolant in cab at startup. Heater core?

This did nothing. There is a faint repetitive noise in the top underneath the intake. Maybe valves? So I've taken off the intake. Pulled the drive valve cover and checked the timing guides. I replaced them about 2 years ago and they still look good. Here's where I'm at now:

10. Replaced thermostat (old one checked out good in boiling water)
11. Replaced temp sensor and sender (in the unlikely event that its just reading cold).
12. Checked resistance on injectors. All between 14-14.5 ohm.
13. Cleaned injectors (a la Fuel injector cleaning without expensive tools - https://www.youtube.com/watch?v=rUUgR94drxg)

Before I stitch everything back up, I'm wondering what I can do to hopefully prevent having to take intake back off.

14. How does one check valves on the SOHC? Just want to make sure they are not bent or broken. Can't find this in Haynes or web. Will I be able to visually inspect them without much fuss?
15. Knock sensor?
16. What else?

Things I plan to do after getting it back together
17. Check for vacuum leak with brake cleaner
18. Test fuel pressure. I know the schrader is at the fuel pump. Can this be done without removing bed/dropping tank (I prefer the former)? Can't find anything in Haynes or web.
18. Came from the factory without EGR, so no DPFE.
19. O2 sensors? Could these cause severe rough run?
20. Cat's? How does one test them?
21. The lingering question in my mind is could water in the gas have caused this?
22. Tried O'reilly's radiator pressure tester, but it leaked at the seal. I'll try my mechanics snap-on if nothing else works.
23. What else?

Put it all back together today. Found a bad pcv elbow up front passenger side of intake. Thought that would fix the problem but it didn't. Sprayed brake parts cleaner over the intake and didn't get any stutter. Still idles fine but chokes down around 2200rpm. Temperature is back to normal with new temp sensor and sender. Makes me wonder if I ran it hot, but I don't have milky oil or coolant.

I'll plan to check the vacuum asap. But how does one check the fuel pressure on the '01+? Everything I've read says the schrader on the back of the passenger rail is not for testing, but a pulse line. That's the only schrader valve I can find along the entire fuel line. Haynes says its in the tank? I'm guessing its electronic? Can it still be tested?

Only things I can think of that are left to check are
1. Fuel pressure
2. Vacuum leak
3. Cat clogged

Is there any way that water in gas could have blown a head gasket?

No, on the water in the gas.

Running Lean with pinging/knocking will eat away at head gasket's soft metal ring, that seals each cylinder to the head, causing it to fail.
But you would hear that pinging/knocking for awhile before gasket would blow.

Generally speaking a head gasket blows from overheating.
Coolant gets low and the head starts to heat up, when heated metal expands, since head is held in place by the head bolts it can only expand down towards the block.
Aluminum heads expands 5 times faster and more than cast iron heads, this was a real problem in the early days with engines using aluminum heads, blown, and cold leaking, head gaskets were very common on early models, even more so if blocks were cast iron.

This expansion of the head metal crushes the soft metal rings between block and head, and one(or more) can fail to contain the 1,200+psi of explosive pressure when a cylinder fires, once the ring is breached it can not reseal, since each cylinder is surrounded by cooling passages, that is usually where this continuing 1,200psi pressure(engine running) is released, this pressure pushes coolant out of the way in the head and since rad cap is only rated at 16psi that coolant is pushed out into overflow tank.
Because the "air" from the breached cylinder is now in the head, and air doesn't cool as well as a fluid, the head gets even hotter, and expands even more, this can crack the head if heated up enough.

Other reasons are failed head bolts, head bolts are stretched each time engine is cooled off and reheated, over time one can break, leaving less holding pressure in that area of the head, this is a rare occurrence, especially with the newer TTY head bolts.

The older 2.9l heads and 4.0l OHV heads did have weak points, and I have read they just cracked one day, not a head gasket failure but same symptom, I have only seen this happen on these engines when they were over heated, but I have read stories from others that it happened without over heating.

4.0l SOHC doesn't have that "weak point in the head" problem

Almost fixed! In desperation went to one of my mechanics today and he recommended pulling the cat out and running. Banged on it but no noise. So I pulled the three bolts from where the Y-pipe connects to the rear cat (#3, 9, 4 below). Ran like a champ and plenty loud. Cleaned out the rear cat (#4 below) by shaking and hammering. The rear cat (#4) was in tact at both ends, but there were large chunks where one of the front cats (#3) had let go of its chuncky ceramic stuff. So I'm thinking the front cats are ruined but the rear is clogged. I cleaned the rear and put it back on and bolted everything back up. It runs almost right but not quite the torque and throttle response as before.
(1) What are your thoughts on which cats to buy? I've got the big stuff out of the rear cat, and its only 3-4 years old, but it may be clogged with fine particles from the front falling apart.
(2) Can the muffler get clogged too or is it just a big box?

That real would be a fluke with those symptoms, i.e. limited RPMs when moving but not in neutral.

The issue with having a Clogged exhaust is simple physics, an engine is an air pump, when you add air/fuel mix and spark it is a self propelled air pump but still just an air pump.

If you restrict the exit for the air(exhaust) then engine can't suck in as much air so "pumping power"(engine power) goes down.
A 4 liter engine pumps 4 liters of air at wide open throttle, with a load(moving) or without(in neutral), it isn't quite equal but close enough.

Which is why the symptoms wouldn't set off my clogged exhaust alarm, lol.

But glad you got it fixed