Pros opinons needed: Clunking noise when clutch is released

[blueapple]

88 Corolla SR5
I bought it from a lady, she drove it without oil for a while and burnt all the crank bearings ( you should see those, they smelled crazy).

Anyways, I bought it for 225 and spent over 2k in repairing it.

But, after I replaced pretty much everything ( except for tranny, which I now regret)
The car has this one annoying problem:
When I release the clutch, there's a clunk or bunce sort of noise. The faster I release the more likely it would happen.
AND! if I keep the car at rest, shit into first ( to stop the gears from spinning) and pull it back into neutral, then release the clutch, there is a small clunking noise, seems to be from the same location.

What I tried so far:
1. Replace the motor mounts, brand new front and back from toyota, OUCH! bitch, they were expensive.

2. Replaced both axles, that helped a little bit, now it's just a solid clunk instead of a "set" of noises.

3. both inner tie rods, they were worn out.

None of them removed this problem and I can't think of anything else now.

The lady seemed to be driving it hard though, when I open up the bell housing, the metal studs were at least 2mm into the pressure plate.
The tranny has about 200K on it.

Could a mis-aligned clutch plate do this?

I'm using beck N arley clutch, which my friend told me that their spirngs tend to break off from the center spindle, and cause "click click noise" But there is no click, just clunk!

might be a worn out differential assembly? I can eliminate this noise by "Squeezing" the clutch and perfectly matching the engine and tranny speed.
But it's a pain to always keep an eye on the tachometer. ( it will clunck is I miss by 500rpm)

By the way this doesn't happen when the engine speed is lower than wheel speed, or say, doesn't happen during down shifts without pre reving the engine, the car dips, but it doesn't clunk.
weird, did I install the clutch disk inside out? Or could be the clutch is just not built to factory spec, so the center spindle is not strong enough.

How long do you think it will last like this?

By the way 5AF engines gets great gas millage, I get 35mpg around town constantly, and I often take it over 5k rpm.