Got a '96 Passport(you know, the rodeo with a H on the front)
4X4, 3.2L V6, 5 speed 115k miles. It's knocking pretty good at
idle, and gets really excessive when giving gas and letting out
on the clutch. Apparently it's not a major problem, it's been
going on for about 10k miles. Was told to replace the pilot bearing.
Replaced clutch, pressure plate, throw-out bearing, and pilot bearing.
Didn't help sound, but drives better. Always seems to be quieter
for a day or so after a fresh oil change. Wondering about
oil pump/pick-up issues or some main bearings but that would not
explain the knocking on the clutch pedal (I don't think).

I believe you might have more than one problem. I do not see how a knocking at idle and then a knocking in the clutch pedal could be from the same problem. Have someone check the motor compartment as you pull forward & backward to try and locate the general area of the problem. Sorry this reply is not a fix for the problem.

Yeah, it's got me perplexed as well.
I do know that they are definitely related because
it is the same "rythm" under the hood and my foot.
Any more suggestions are greatly appreciated!

maybe something is busted/broken

Could this be the old worn out timing belt tensioner knock thing? T-belt slaps against a t-belt cover. Sounds like a rod-knock. Pull the t-belt covers & see if the noise goes away.
G/luck
Joel

The t-belt and all associated components have been visually inspected and seem up to par. Still looking for the top of my right index knuckle. Didn't actually remove the push-rod tensioner to check the tensioner and idler bearings but, pretty sure thats not part of the problem. Still searching and brain-storming.