When installing the SC to the manifold it is very important to do it properly. Here is the procedure I use:

1. Use form-a-gasket and create about an 1/8" bead around the surface of the manifold (keep it a continuous bead around the center of the non powder coated surface, see the yellow lines in the photo below).
   
2. Thread in (just a couple of threads) one of the stock intake manifold studs (you removed previously) into the #3 position. This will help you center the SC when you go to insert the bi-pass nipple of the TB adapter into the bi-pass hose and drop it down over the stud.
   

3. Insert and thread down (just snug) the #1, #2, and #4 mounting cap screws
    (a  "T"  handle Allen wrench works nicely here). 

4. Remove the stud from position #3 (I used a channel  lock pliers).

5. Install the last cap screw and try and snug all of the cap screws to
    an equal snugness.

6. Now, going in this pattern: #2 then #3 then #4 then #1 start tightening in 1/4 turns all the while turning the pulley on the SC. Keep doing this until the cap screws are as tight as you can get them with one hand using the "T" handle.

If you detect any change in the ease with which you can turn the pulley while tightening the cap screws, STOP TIGHTENING!!!! The pulley MUST spin as easily throughout the tightening process as it did before you started. Any restriction in this spinning is evidence of case deflection (The screws/rotors are making contact with the case and this is an absolute NO NO )!!
If this happens, back off the cap screws a couple of turns and start over but change the pattern of tightening . In other words try a different combination of numbers, but try and keep them in a criss/cross pattern. If you exhaust all the possibilities it's time to call Bill.

DO NOT (repeat NOT) attempt to start the car with the SC case deflected, there can be NO restriction on the ability of the pulley to spin-- NONE, ZIP, NODDA!!!!!!