Clutch Spring Installed Correctly

Clearly, something is wrong. The spring in your picture does not hook that way. That little slot in the fork is a hook point, making a tab that would be attached by the z-bar pivot would be the other. Does the RMS mount attach at the engine, or did you use the stock motor mount and that attaches to the RMS mount?
I have this same set up. I do have a Centerforce II diaphragm clutch. I had to do some altering to get it to operate smoothly. Plus, you say the alignment is off on your trans. If that is off, so is your clutch linkage.
Can you get a second pair of eyes to look at it? Your missing something. You can only do so much here.