OK, trying to separate and address each item but still group somewhat together...
the old clutch you say was a 3600lb unit and worked fine for years. a swap of just the clutch and you now are bending/breaking linkage. the old clutch was installed with the incorrect fork? or the new clutch was installed with incorrect fork?
what size is the new clutch and flywheel? with the right bellhousing it'll be a 10.5" unit. what brand of flywheel did you buy? it's very possible the flywheel you bought is thinner than what's needed and the geometry is still off.
what brand of T/O bearing did you buy that is tall? there are only two that i'm aware of and one is incorrect. the only correct bearing is a G1625C.
the left bearing is the std (old number) CC1705C/614018 (new number) the unit on the right is a Six cylinder unit with a rounded face for use with a flat diaphragm clutch... the center bearing is the only tall bearing.
which did you use?
the adjustable pivot, there again are two styles, the std style which covers both of GM's bell housing pivots, the other by McLeod, which will handle a higher adjustment than the factory style pivot.
left & center are GM pivots, right side is the McLeod unit. the std style adjustable will only adjust as tall as the center factory pivot.
which pivot was used?
with the incorrect fork even using the adjustable pivot and a taller T/O you wouldn't have been able to correct the geometry and it's possible the strain has weakened the new Zbar.
use the correct fork and the adjustable McLeod pivot and the new clutch assembly with the recommended T/O. i think what you may have is a thinner than needed flywheel which moves the clutch closer to the engine effectively taking away any level of proper adjustment...
you can pull the front bearing retainer off the trans and with the engine on a jack, place the engine/bellhousing at the proper level to install all your linkage. install the T/O bearing on the bearing retainer, with a clutch alignment tool or extra input shaft, install it all in the back of the bellhousing and connect/adjust the linkage. you can climb into the car and actuate the clutch... if the adjustable pivot needs to be adjusted you're not repulling the trans, an adjustment is quick and easy.
some aftermarket ChevyII pans are cheaply made... a big name like Moroso, Milodon, Hamburger etc will have a pan with a better cut out area. the centerlink will raise and lower as the wheels turn so that cut out is necessary on that style of pan... the Kevco pan is a rear sump pan specifically designed for a ChevyII but with no cut out for the centerlink.
back to the clutch for a minute... i can appreciate a possible mount issue, too short, too tall... my thoughts are the clutch worked fine before so i'd not think the mounts are an issue...
sorry to be long winded, hope i covered the bases and have helped... check some of this stuff out and we'll see what we can do...