My son's 89 F150 4.9 5spd, 106K mi. Two issues:
1. The vehicle makes a rumbling sound probably around 3500 rpm (that's
a guess, no tach), whether the clutch is in or out. Any guesses?
2. It has a slight miss. We replaced the plugs, wires, dist cap and rotor (Autolite on the plugs & wires) and symptoms are the same. Thots?

 

Have you pulled the codes on the EEC?

Have you checked it for vacuum leaks?

Sounds like you've addressed the ignition basics.

The 'rumbling' at high RPM may be lean mis-fire. This, coupled with the miss at idle, sounds like a vacuum leak somewhere. A vacuum leak may or may not generate a code or turn on the CEL. Only if the leak gets severe enough to indicate a lean condition that the EEC cannot compensate for will you get a CEL or lean indication. The miss will show up LONG before it gets that bad, and it will drive you nuts before it sets a code. I have a 5.0 in my '92, but have a peek at my gallery, and you'll see what was generating a miss at idle, and an unbearable shudder at highway speed.

 

We'll check it for vacuum leaks. Thanks.
BTW, there is an apparent draw on the battery. No interior lights
or anything obvious like that. The radio doesn't work. I'm thinking
of pulling it to see if it might have a short.

 

You sure the glove box light isn't on? Can't see it with the box closed, but my switch mount broke on my truck right after I got it, and I got it replaced under warranty. Funny part was, it broke because the owner's manual was in the pocket inside the box, and hit the switch when I closed it the first time.

 

I took it tonight to a friend of mine, who is a Ford mechanic. He found a vacuum leak, which he fixed. Still rumbles a bit at high RPMs, but not as bad. He also found the battery drain. The alternator was putting out 14 volts, but with the key off, there was a 12 volt drain on the battery. Disconnecting the alternator dropped that way down. So apparently a diode in the alternator is shot. Finally, he thought the miss might be a semi-plugged fuel injector. He suggested putting a bottle of fuel injector cleaner in the gas tank.
So, most mysteries are solved for the moment. Thanks for the help.