Slant six with modifications runs horrible. What else can i do?

Start from the begining and go thru the tuneup.Just check everything if the parts are new. Include a proper valve adjustment and check for vacuum leaks.As far as the MSD make sure to use the proper plug wires and up graded coil. I had problems with missing and ruff idle with the stock mopar electronic wires and coil when I installed the MSD 6A.
Most slanters are using NGK box stock# 3459 spark plugs. The # on the plug is different than the box # and I can't recall. If all checks out then try different timing settings.This is just a start as much more can be involved.
This is just for reference your results may vary.