Good, methodical diagnosis. Well done. The S4 appears to be working correctly. Try posting in the Split Second forum, perhaps someone familiar with SS has had a similar problem.
In the meantime, I would strongly recommend the following: (1) Throw all of your DIN plugs into the nearest trash can (2) Place a call to Fred at Phoenix Sports and order a TIDO or an OC-18. For a few hundred bucks you will get yourself a simple, easy-to-diagnose, straightforward wiring solution and rid yourself of a lot of the mystery surrounding your timing setup.