How much tolerance is there in the length of a driveshaft? and how far does the slip yoke need to be inside the transmission?

Look at the yoke. The darkest wear spot is the normal ride height position. The clean area is the typical range of travel. They usually go in about 2.5". Any less and the yoke won't ride all the way in the tailshaft bushing. Any more and when the rear suspension compresses you can slam the yoke too far into teh trans and break something.

would the slip yoke be the same length on a 90 700r4 and a 93 LT1??

It should be. The driveshafts are interchangable. The '93 uses a 4L60E, which is just a 700R4 with fully electronic shifting controls.

well i did the t56 swap and i am getting this clunking sound that happens when the tranny moves around from torque like if I'm in gear and coasting and I tap the gas. I had the tourqe arm off and was able to recreate the sound by pulling down on it which pushed the slip yoke in and cause the sound. So I was wondering if i should have used the slip yoke that came with my t56.

If you are using an LT1 T56 it's the same yoke. If it's a retrofit T56 then the driveshaft has to be shortened about 1.9"