Possible rod knock?

Well, I guess we can rule out flex-plate then, lol.
But that then brings crank end-play back, as every time you step on the clutch, the thrust-bearing takes the hit.

This is an easy test,
What I do is climb under the car, and remove the flywheel tin, then stick a prybar up there between the flywheel and the pan, then take a prybar in your other hand and stick it between the balancer and the pan.
Next, pry the crank one way then the other. if you hear the deep thunk-thunk, then you better measure it. IIRC it should be more than zero, but less than .010
If this is your problem, fix it ASAP, cuz eventually the flywheel will grind a groove into the rear cam plug and boss, which is gonna cost you more money to fix, ask me how I know, lol.