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I did a leak down compression check and no blow by in valves or rings i lapped the valves when i did the rebuild.
You did a leak down, checked cranking compression, or both? Is the plug wetting with fuel? Does a noid light flash on that injector connector?

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Just a leak down have to order noid light. Plug not wet with fuel but blackened from being too rich
That makes me think it's a compression issue, you can burn a little and make soot but not contribute to the engine running. I would check cranking compression just to cover all the bases. If you disable fuel and crank the engine does it sound like it's skipping over a cylinder or does it crank normally?

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Recirc or not shouldn't make cyl 3 misfire especially when not in boost, it sounds like this is an all the time misfire and not just an on boost misfire. Nor should a different MAF make one cylinder misfire.

May also be worth while to try swapping the resistors between injectors, double checking they're all the same resistance, and swapping the injector between cylinder positions. I like to swap parts over more than one cylinder, like if Cyl3 is the issue I'd swap it to cyl 1 not to cyl 2 or 4. That way it's further away from the possible problem and you can more solidly know if the problem went with the part or the problem stayed with the cylinder. One more thing to consider would be the possibility of Cyl 3 being lean due to a vaccum leak at the injector or the intake manifold port on the head.

So if this were in my bay at the shop I'd do things in this order to diagnose a misfire.
0. drive vehicle to ascertain exact conditions of misfire, all the time, only at idle or only under load, hot/cold, etc.
0.a verify which cylinder is misfiring by pulling plug wire or injector connector while engine is running if it's an idle misfire, have seen engines with multiple weak cylinders throw misfire code for wrong cylinder due to slowing and speeding crank shaft speeds. Usually the actual misfire is the cylinder before the indicated misfire in the firing order when this happens, seems to most commonly be a Ford issue.
1. check spark with plug out of cylinder and grounded to head to verify plug works and coil works.
2. check compression on cyl 3 and cyl 1 for a comparison, if needed follow up with compression check on cylinders adjacent to problem cylinder to check for compression bleeding across to another cylinder (unlikely with a single cylinder misfire), if low possibly leak down test to determine where loss is happening but at that point mechanical issue means engine needs to come apart anyway so who cares it'll get seen when apart so a bit of a time and money waster. Maybe pull valve cover to visually inspect for busted valve spring or something.
3. swap ignition coil from 3 to another cylinder, waste spark setup means you only get 2 coils so swap from cyl 1/4 to cyl 2/3 but leave the wires in place.
3.a swap wires/plug boots around if possible (not possible with cyl 1 and 3 sadly) and inspect closely for burn through and arcing.
4. swap spark plugs from 3 to 1 and vice versa, inspect closely for arc over on the ceramic insulator and other visible issues.
5. smoke test intake system to check for vacuum leaks, possible for idle misfire which improves as vacuum decreases when accelerating.
6. check injector signal with noid light for good bright quick flash that gets faster with engine speed and remains bright.
7. swap injectors between cyl 1 and 3, compare resistance values of all injectors to look for borderline values or out of spec values. Inspect sealing o-rings for damage closely.

One more thing to check since you did engine work would be the valve clearances but this isn't part of my normal checks since it's uncommon on a previously normal running engine. If something went wrong and the intake or exhaust valves are not opening enough on that cylinder you can have pretty good compression, no leak down, but poor combustion and misfire due to a low amount of air entering or (or leaving, exhaust won't burn again) vs the amount of fuel being added. That could look like a rich cylinder but not be a fueling or spark issue. It should show up as a bouncing vacuum gauge when cranking the engine with closed throttle or with the engine running but vaccum is funky on a 4 cylinder with a dead cylinder.
 

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CKP ring flipped over, haven't seen that in a while! I recall it causing no crank or running really badly, spark/fuel timing didn't coincide to cylinders at TDC. I don't remember it causing one cylinder to misfire.

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Probably easier cheaper to just grab a used ECU and flash out the immobilizer. Open the case up and look for visible damage tho to clue in to what caused your failure, make sure nothing is shorted and check how many amps it takes to open the injector.

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Well you're assuming the ground control side is dead from the PCM, make sure that injector is getting power. Could be as dumb as a pinched or broke wire feeding that injector power.

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So just to go over basics here so we're all working the same knowledge set let's review how the injector circuit works.
There's a fuse that powers the injectors (and probably other things) that's running on a common wire to the injectors for shared fused power. The ECM pulls that +12 down to ground one injector at a time to turn it on. You should be seeing constant power at one wire with the ignition on and ground turning off and on at the other wire with the engine cranking or running. The noid light needs BOTH power and ground to light the bulb, the bulb not lighting does not automatically mean the ECU is not grounding it if you're only probing the injector. You need to connect the noid light to B+ AND the ECM injector control circuit AT the ECM connector via a backprobe to know it's the ECM. The noid light not lighting at the injector still leaves the possibility that injector power is the problem due to a broken or corroded wire somewhere. You should at least ohm check between the injector connector + terminal and the fuse and see low ohms, usually OEM's want under 5 ohms on circuits like that. The ECU should be the last thing to replace when throwing parts at a problem since it's a big ticket item, you want to be sure.
 

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I'm going up against a similar situation with my Celica and an intake manifold install trying to make it 107% perfect like if it was stock, I feel ya man! Battling with some slightly high idle currently and ended up finding out my Q45 throttle body was bad, had been apart and back together BACKWARD. WHO DOES THAT? Always some shit and never normal stuff.

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Unfortunately I know nothing about that, I could only refer to search here as someone has probably had a similar enough issue to yours to get you going.

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