2012 Ford Transit Connect XL CNG nightmare

Hey Scanner Danner community!!     
‘12 Ford Transit Connect. CNG only equipped fuel system. 60,000 miles. Idles for 1-2 minutes and stalls. Misfire code cyl 2 Changed fouled/seized spark plugs (fixed bad thread)  Changed oily fouled coils NEW Code is gone.     No codes anymore but still not running right.  Changed fuel injectors OEM Bosch CNG specials new   One was fouled, all of them kind of….rusty?   Changed pre regulator CNG coalescing filter, old one was clean, no residue in reservoir. Got sufficient fuel pressure at fuel distributor bar by ear when I disconnect fuel line.   Sounds like around 90 psi when I disconnect, like a nail gun??    No valve anywhere to check that pressure.  Changed valve cover and gaskets, where water had corroded the head and let oil in to plug holes (noted very clean cams and oiled innards & parts)  Notice that the windshield wiper spray ports are holes in the hood directly above the valve cover, and the battery. They drip water when it rains. (Also over the EGR valve, which I will come to learn about) Cleaned mass airflow sensor Cleaned throttle body Cleaned T-MAP sensor Checked compression !!! (good on all 4 cylinders) 180 psi phew Smoke test right after air filter: leaky EGR, found bug sitting on the valve inside the EGR.  Changed EGR Valve assembly (that got it back running more than 1 minute and back limping around)    Noticed/remember that coolant was low from what I now know was jacked up EGR and topped back off.  Changed intake manifold gaskets, EGR gasket, cleaned EGR tube Intake manifold was oily inside. (PCV?) Cleaned out with degreaser and dried out.  Intake valves on cylinder 3 were oily/wet. Cleaned with brake clean and zip ties, figure it was from possibly leaky PCV valve?  PCV valve doesn’t maraca is loud or profound as new one. Cleaned a bit of carbon off of valves but wasn’t too bad at all. No gasoline to clean them while it runs on CNG/methane but they weren’t too bad for carbon except for oily #3.  Changed PCV valve and hose to new OEM. And Gasket!  (Inspected oil separator, very nice and clean oil in crank case and bottom of separator.  Changed upper motor mount. Old one was pretty loose but not broken.  Changed new aftermarket spark plugs to OEM Motorcraft just to be good.  Checked timing. Tight chain, cams perfectly positioned and taught, crankshaft pulley in dead nuts correct position.  Noticed cracks in harmonic balancer rubber so changed it, (12 year old truck this year) set it at exact timing torqued to spec. Reinstalled crankshaft position sensor pointed directly at pulley tooth in TDC compression.  (Changed idler and tensioner pulley on serpentine while it was off, both just about gone/noisy.) (Noticed multiple power steering leaks but will top off or change and that’s for another time.)  Smoke tested exhaust. 3 holes in bottom of muffler. Not big though. Drain? Got quite a bit of smoke out of resonator but out of weep hole. No other leaks. And absolutely NOTHING up by engine. Tested low pressure at down stream O2 sensor port. Just hovering at 0-1. Couldn’t get upstream off because it is totally welded in. (Hmmm) And I know why now.  Tested vacuum at front of intake manifold. It’s super low at idle and slowly goes lower until it dies.  So the not cooling halfway stuck open EGR was spraying heated oil mist through the combustion on valve 3 and fried the first cat, obstructing the exhaust. ?? Exhaust manifold gets super hot. It’s all orange. It had been “steaming” for a while.  Changed exhaust manifold, O2 sensor, and catalytic converters.  Tested back pressure at upstream O2 port and it’s fine, until it’s not and it jumps up to 6 lbs before it stalls. At this point I removed the cylinder head. I took it to Michigan Motor Exchange. They confirmed that the valves were “shot”  I noticed they were very rusty and assumed there was a problem. They changed and reseated all valves and re surfaced the block mounting surface.  While the head was off I changed the  alternator, thermostat and water pump.  I cleaned up the power steering pump and fixed a leak at the low pressure hose mount ostensibly. Reinstalled the head and was acting the same way, barely any power, stalling at idle, I got it on the freeway and got two cylinder misfire codes and 2 and 4.  I figured I’d damaged some valves retiming the engine so….   Took the head BACK to Michigan Motor Exchange the walk of shame, they pressure tested it for me and it checked out fine.  REinstalled cylinder head.  No change.  At this point im still suspecting blocked cat and put a new one on that I had.  But still testing with exhaust disconnected at manifold so wide open basically and it’s actually the same, stuttering etc…      I changed the original downstream cat thinking it’s telling the computer to do funky things.  This all leads me to the fuel system being my last option.  I ordered a new luxembourgian regulator from Rex. There was stinky water in the old regulator, which got quite wet when it was running from condensation?   First time I’d noticed this though. Changed regulator and cleaned out old post regulator filter bottle. About two tablespoons of oil in the bottom and filter element was cracked and hard.   Left element out.   Installed shrader valve to check fuel pressure where the bleed off t was before stock fuel line up to rail. Checked fuel pressure 110 PSI per spec and right there while running.  Went to the computer.  When running decent, STFT is oscillation up to 5%.  LTFT is up to 20%     Finally after a time      STFT is jumping up above +20%   And it keeps trying to die and trying to stay alive until it’s just stalls.   Dead.   MAP is reading 50 kPa    If I give some RPM/gas that goes down to 35 kPa?       

At the risk of sounding rude, there's just too much here. It's hard to tell even what the symptoms are. I appreciate the thorough service history, but it's really confusing.
If you can consolidate it down the symptoms, the tests performed and the results (like "back pressure is fine until it isn't", "fine" is not a measurable value), (you said you it sounded like 90psi, near the beginning then near the end you said you measured 100psi. You could have just said that it has 100psi fuel pressure), then you will stand a much better chance of getting helpful replies from the community.

I’m apologize I’m not a professional mechanic. I mentioned the fuel pressure sound because that was before I installed a shrader valve on the line. There wasn’t one at that time. The measurement of 110 came off of that after I’d maintained/updated the fuel system, new regulator, some new fittings, new module etc….     

the exhaust back pressure is hovering right between 0-1 psi until it starts to hesitate and stall out.   Then it will jump around 5 or 6 psi and that is at the upstream O2 port.  

I guess the symptoms are:  it runs not very well until it hesitates and eventually stalls out. Compression is good at 180 on each cylinder. Vacuum is solid at 15 inches which is low to me. 

I’ve got misfire codes at the beginning and recently when I tried to drive it on the freeway. Recently I got a lean code but I had the O2 sensor disconnected when it happened and it never happened before. 

I realize I’ve probably gone about this in the wrong way from a professional’s stand point. I really thought it would be as easy as getting the fuel and plugs right…Now I just need to get it going. That’s why I’m here. I need some smart help and using this scanner to actually find the cause that’s hindering the function.  I’m looking in to upstream O2, the brake booster vacuum and possibly my main fuel line being obstructed today. 

I really appreciate you having a look!!     
 

Thank you for not taking offense to the previous post, it can be difficult to judge intent and context in the absence of body language.
I agree with you, 15" of vacuum is too low. If this is the engine I think it is, it is possible for the camshafts and crankshaft to be misaligned, all though the target wheels may be in perfect sync.
Did you use all of the appropriate locking tools during the job? It is vitaly important that the correct crankshaft locking pin is installed in the back of the block behind the axle shaft, and that the plate that locks the camshafts together is used. A mistimed engine would explain most of the symptoms you describe.

Yes. I’ve checked timing and timed the engine when I reinstalled the cylinder head. I use the bar to get the cams perfect, the pin that sets top dead center on the drive shaft, everything torqued to spec, new driveshaft bolt and slip washer etc..       check timing it’s perfect.   Everything inside the engine is clean and no sludge at all if that means anything, I’ve kept pretty good on oil changes the whole time I’ve owned it. 

I checked the brake booster yesterday by plugging the vacuum outputs from the intake that go to it.  No dice.    But I’m convinced now that my damaged fuel regulator damaged the fuel injectors with way too much fuel pressure and damaged the new ones I put in at the beginning of this nightmare.  Before I replaced the regulator.    The tanks hold up to 3600 psi so if the regulator cracked and was letting by high pressure I’m convinced that could damage the tiny injectors.    But we’ll see!!   New injectors landing today!  

I appreciate you taking the time and brain power to look at this!!