Classic/Antique Car Repair: Ford 289 misses on 2 cylinders, vacuum leaks, vacuum leak

Question
Hello

When I started my Mustang this spring it fired up and ran well immediately.  A short while later on the highway I noticed it was missing.
It is a recently pro rebuilt 1966 289, 4V, auto, stock except Pertronix and dual exhaust.

My mechanic (40 plus yrs experience)says it's missing on #4 & #6 and has checked literally everything.

Changed plugs\wires a couple of times, checked timing, changed back to points, cam out and measured, valve train checked, compression good, exhaust clear, changed carb, magnaflux intake twice, checked for vacuum leaks with propane and consulted with every grey haired mechanic in town, and likely a few more things I can't remember.

Is there something obvious here we're not seeing?
Any help appreciated,

Thanks,

Peter

Answer
I am not sure that I can give you a direct answer but I might lead you to the answer. First of all number 4 and number 6 use the same intake manifold runner. Number 6 and number 4 are seperaited by number 2 wire in the distributor cap so I think that we car eliminate a crack in the distributor cap. My first step would be to find any vacuum lines that are tied into that intake runner that feeds number 4 and 6. I would then block those lines and road test. there could be a vacuum leak in one of those devices that draws vacuum. I recently had a rambler with a skip in number 5. It turned out to be a defect in a Marvel Top Cylinder Oiler installed on the engine. I do not have one of those manifolds in front of me so I can't tell you what is installed. The other thing that I would do is to read the color of the spark plugs after a road test. Also a sticky intake valve on number 4 could cause the problem but it should effect number 2 as well.
Please keep me posted on this. Brad