CEL flashing, bad idle, severe misfire, P0302 P0316, compression test results

Evo, I of all people understand your pain on this giving my most recent issue that I myself posted up help for and it ended up being what was in the back of mind the whole time. Problem with getting help on the net is that with us not being in front of the car we can only give suggestions that with hopefully lead to a fix.

With that said. Let's be honest. You have pretty much gone over every aspect of this Mustang. So lets look at what you have not fully gone into.

1. Compression numbers are a little on the low side. Not saying this is your issue, but it is there.
2. At this point everyone has tried to get you to look at the engine harness in detail. I personally think this is a great place to start.
3. Only one head got looked at and "fixed". Both should have been pulled and serviced to eliminate any doubt.

You have done a great job on your own trying to figure this out. Most people would have givin up a long time ago. I was getting pissed off at my issue but I would have kicked my own ass if I sold it out of frustration and the new owner fixed it as easily as I did in the long run.

To go one step futher. I have an Alldata DYI account I would be willing to give you access to that may help you with this "possible" wiring issue. My car is a 96' however (no COPS) so I dont know how much it would help you. BUT you are more than welcome to it.

Stangnet has some of the best folks on here!
 
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Yes, I got the cylinder head back from the machinist and put on the engine.

I *think* I've got the timing set correctly. I'm going to take some pics and post it up and kindly ask for some verification.
 
Here are some pics of the timing chains attached to the engine. The crankshaft is held into place by an OTC 6024 crankshaft holder tool. When this is installed, the keyway is at "10:30" and #1 cylinder should be TDC. I had the motor placed at a 9:00 keyway in "safe mode" when I installed the heads and rotated the camshafts to get them close to the timing chain marks (or where they needed to be).

I pulled the chains out and marked them at their ends using BLACK for the driver side and PURPLE for the passenger side. I then lined up these lines with the "dimples" on the crank gear and the cam gears. They are located at between more or less 11 o'clock and 1 o'clock. Please see pics for verification.

I turned the motor over by hand a few times and did not feel any resistance like PTV issues. I heard the cylinders compressing and then bleeding off as the motor rotated.

I want to make sure I have the timing set correctly before I proceed any further. It'd be much easier to correct for off-timing now than before I start the motor and destroy it if something is incorrect.

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NOTE HERE: in the photo there is what appears to be a dark colored link a few links away from the cam dimple. This is just a camera illusion, the link in real life is uniform in color to the rest of them. I am SURE I have the driver chain marked half way because even though the sharpie wore off there was an upside down "USA" marked on that link and not another upside down USA for several more links. I checked, rechecked, and triple checked the number of links away from the cam dimple to the crank dimple.
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last time you did ok...if you dont want to turn it over ??????????times to see if marks align again...

notice tdc on crankshaft...and dots on camshaft...dots should come back into alignment every other rev. of crankshaft ...

was anything found wrong with the head????

any wires found shorted in engine harness????
 
The head didn't have anything obviously wrong with it but was machined anyway just in case.

I took the harness apart but didn't find any issues with it.

I'm not messing with any more electrical tests, I'll let a pro do that
 
I bought another car as transportation and have been dragging my heels on repairing the mustang.

I'll get there eventually.

I was working on it today and noticed that my passenger side valve cover has a crack in it so I'll have to find a replacement for it before I can do any more work.
 
Been meaning to reply to this but I just now felt like using my PC as I just had a major surgery done after yet another 2 weeks spent in the hospital. Anyway, I'm glad you got this mostly sorted out and hope the car stays fixed for a long time. I remember when I was trying to hunt down my mystery problem and how damn frustrating it was to hunt down but when fixed it I was releived.