You gotta give us a little more info there.

1st. engine rebuild.....was the ms&s running the previous engine and how was the idle?

2nd. if running spark did you tune the VE before you hooked up the spark to the MS?

3rd. Have you tried hooking the new built motor to the stock fuel system?

Checked for the obvious?.....vacuum leaks, cam timing, connected the IAC and all harness conns?

That will help a little