What am I missing? Can't figure out a 351w miss

I will add pics after I write this, so if you see no pics, they'll be here soon.

351w, fresh, basic rebuild by yours truly.  I took my time and think I did a good job. Not sure if that means that it is awesome or that everything is sketchy or not....  Nothing fancy, nothing special.  Basic or standard replacement pistons, cam, etc.  It has about 1,000 miles on it now. the heads were built by a guy in Texas who is known, reportedly, to be one of the best head builders in the state.  Not sure if it's true, and even the best can make mistakes, but chances are they were built properly.

It fired right up initially after figuring out that I had turned the engine over once to tighten the torque converter bolts and ended up with the dizzy 180 out.  Frustrating because I was very aware of that possibility and thought I had taken sufficient pains to do it properly.  Oh well.  But that meant that we had several rounds of cranking it over to try and start and then try and diagnose before getting it right.

Ran it at about 2500-2700 for 25 mins upon initial startup with actual break-in oil.

It has run great until a few months ago I'd say.   I remember feeling a slight miss or hesitation at times, but the transmission seems to have some issues so I've always just assumed that any bad feelings were from that since the motor has been solid.   

It also has fitech throttle body efi which gave me issues initially but I took some steps that seem to have fixed the issue and it's been fine (i think) since.   nothing at least that says it is fatally messed up.  It also has a pertronix electronic ignition unit that replaces the points and condenser.

Well, the slight miss has got worse and I started doing some proper testing. I don't have a tach in there, so i ran with the handheld computer and watched the digital rpm readout and when it started missing, the numbers would go 2200-1100-2250-700-2300-1800-2350-1400 etc.  Not exactly those, but you get the idea - it jumps around. But the motor is definitely not jumping around. The signal or the computer's interpretation of the signal has an issue.

As far as the behavior, I was able to nail it down to this: it starts at about 2200 with light throttle and as you gently toe in, it gets worse and worse as the revs climb until about 2800 when the missing gets really bad and then suddenly clears out and it revs just fine.  if you get heavy on the throttle it blasts right through that as well.

So I put a traditional tach on it to see if the problem was the efi or the ignition, and it was definitely not jumping around like the fitech's tach.  I have a video I'll try and link.  

My neighbor came over while I was futzing with it and immediately said, while it was idling, that I had a miss.  Sure enough, I actually had two dead holes at idle - number 7 and number 4. They are 180 out in the firing order.  Seemed like an easy case of swapped wires, but we tripled-checked and it's not (keeping in mind ford's numbering system and the proper firing order for the 351w). Besides, the problem seems to have crept up - at the very least, it has happened without me touching anything under the hood as far as I can tell.

I have done the following diagnosis and testing:

The miss at idle is definitely two specific cylinders.   swapping wires doesn't move the miss, and I ohmed the bad two and two good ones and they all were the same.

I did a compression check and the two bad and two good cylinders are 175psi

I swapped plugs between a bad and good cylinder with no change.

the plugs from the dead cylinders were not wet. doesn't mean anything exactly, but they definitely weren't soaked.

The plugs all look about the same - very white. you can just discern a little more grey/tan on the good cylinder plugs but it takes a keen eye to see it.

the cap and rotor looked pretty good but I cleaned them up anyway with no change.

Tried my neighbor's spare coil with no change.

the pertronix has a little sensor that has 8 magnets that trigger the unit. I rotated that 90* I think and the misses stayed in the same cylinder.

We used a spare plug in #4's wire and laid it on the valve cover and it fired.  doesn't mean it's firing in the cylinder, but it's firing out of the cylinder at least.

I pulled the pass valve cover hoping to find a rocker stud backed out, or an adjusting nut awry, but everything looked great.  I haven't turned it over and measured the collapsed length of the valve springs to see if the bad cylinders maybe have wiped lobes and aren't opening/not opening enough but both valves on #4 are moving what seems to be the same amount as the others.

there is no glitter in the oil.

I know this is a novel, but I'm trying to figure out what could cause it.  Here are some of my thoughts. am I off?

Fuel:

The efi is throttle body and I can't see how it could cause misses (at idle at least) that are only two specific cylinders.  I'd expect misses that move around.

Maybe a vacuum leak on those two cylinders, and I forgot to spray starting fluid around before I pulled the cover off. but it could be leaking in the engine valley. but the plugs aren't dirty like i'd expect if it had a vacuum leak in the motor and I don't hear anything which it seems like a vacuum leak significant enough to kill a cylinder  would be audible.

I don't think it's fuel, at least not the miss at idle.

Spark:

Same with the ignition - Only the sensor on the shaft has anything to do with what cylinder fires.   apart from bad magnets, I can't see how it would cause a miss that stays on two cylinders.

I've moved plugs and wires and tried a different coil and moved the sensor around all with no change.  The cap LOOKS good but is the only thing left that deals with specific cylinders that i haven't eliminated.

valvetrain:

short of measuring, everything LOOKS good. No ticking indicating excessive clearance, the valves on the side I pulled the cover look good and seem to move properly.

I don't know if the miss at idle is the same issue as the stumble at light throttle at 2200-2800.  I assume it is, but maybe they're separate?   I'm tempted to replace the pertronix but can't figure out how it would cause issues on two specific cylinders since rotating the sensor didn't affect it.

any thoughts????

When you disable the spark and crank, does it go ruh-ruh-ruh-ruh-ruh-ruh-ruh-ruh or ruh-ruh-ruh-wheeze-ruh-ruh-ruh-ruh?

An educated ear can hear low compression.

As an aside, those are some super long rocker studs.

As I recall there were no irregularities when cranking with no spark.  The two bad and two of the good cylinders are at 175psi. 
 

here are the plugs:

While they used to be great I've had nothing but trouble with Pertronics stuff lately.  I'd swap that out before I went any further.

Did you by any chance check if the plugs in the dead cylinders spark? Although the fact that they're not wet would suggest spark might not be the issue.

This very much sounds electronic to me- but not a throttle position sensor as I originally thought. Are you getting a ground out of a wire when hot or crossfire? That coil is made to go sideways...correct? 

In reply to BoxheadTim :

I swapped plugs between a dead cylinder and a good cylinder and the miss stayed the same. 
 

i, maybe shortsightedly, focused on one of the two dead cylinders and primarily checked and tested our changes on number 4 and rarely on number 7. 
 

I figured that it's probably the same thing causing both cylinders to miss so if we changed something on 4 and it didn't work, no need to try on 7  

But who knows - maybe we have two different issues and I should have checked both whenever we changed something. 

In reply to grover :

I'm of the same thought but am still suspicious of the valvetrain.  It could be fuel, and maybe the stumbling is the tps.  In fact, I'm going to see if it gives me a clean reading throughout the sweep.  
but I don't think it's my idle miss.  Could be - maybe I have two issues.   I'm glad you mentioned it and I'll research how to get a reading. 

How is your alternator V? I think you mentioned at higher rpms the miss was gone. At high rpms the alternator output  might be higher & good. At low rpms if the V is low then that might do it.

I second the pertronix as suspect. My dad had a very similar issue in an AMC 390 recently.

I start every troubleshooting session with a new set of plugs. After chasing a misfire that I knew was a carburetor for days, a set of plugs solved the issue in 10 minutes. Plugs are a lot cheaper than my time.

From there I'd be thinking the EFI is a little too lean. A miss at idle and a mid-throttle stumble make me think it's running out of fuel. Is there an easy way to add fuel?

Its a Ford with throttle body EFI....put tinfoil or a cookie sheet between the distributor and throttle body just to make sure its not electrical interference.  The Holley Sniper systems have this common problem so I suspect other budget EFI systems with the ECU built in would too.

May not be the problem but easy to test.

I rarely ever had a vacuum advance can on an SBF that worked right for long; they can cause problems statically and dynamically.  Distributor springs can get slacked out as well, then manifest as weird mystery problems.  Usually, it will run better if you take off the vacuum hose, however some version of efficiency may decrease . . .

Dont know anything about a 351W or electronic ignition doohickeys, but have you checked your timing/advance? Could it be something clogging your carb jets on the poor running cylinders? 

I had to clean my carbs 600 times (okay maybe 5) to get rid of some teeny deposits that were effecting some of the carb jet ports ever so slightly. Again these may be horrible suggestions but thought it was worth it.

Appreciate the thoughts and ideas...

the voltmeter says 14.1 v when it's running. 
 

I did have a problem with the efi that the manufacturer said sounded like interference so I put a grounded shield around the signal wire and that problem didn't come back.  It could still be an issue though...

it's not a carb so not dirty jets but it could be dirty injectors....  

I'm at the point of just replacing stuff, but I don't have much stuff around to replace with.  So maybe I'll just get a new ignition and try it....

Thought I'd share the cause of the problem. Turns out my brake booster is leaking and causing a vacuum leak. The vacuum is from a port on the manifold that is on a runner that feeds - wait for it - cylinders 4&7, the two that were missing!
 

now I'm looking into doing a hydroboost conversion since I'll be dropping some money on it anyway