Clutch fork won't clip back in.

I just use a ground .310" plate bolted between the flywheel and clutch cover. A 1-2" depth mic is what I measured with. The three eyebolts on the cover make the adjustment. They are likely "staked" to prevent backing off in use. You'll need to "re-stake" if you adjust them. I found my new cover was out over .050" on one finger.
That said, I can't imagine the lack of clearance unless your new cover is deeper than the original. Have you checked that?

I see two different length release bearing on Brewer's for the 18 spline....................

http://brewersperformance.com/products.asp?cat=31