If I have a safe harbor plan that isn't ACP safe harbor because of after-tax contributions, then how do I complete the ACP test? Do I include just the after-tax or do I include the SHMAC as well? What if it's not ACP safe harbor because the SHMAC and/or a regular match exceeds the prescribed caps? Do I test only the match that exceeds the caps or the entire combined matching contributions? Please list any and all available options and site regs if you can.

Didn't your teacher make you memorize section VIII.F "Continued Application of the ACP test to Certain Conditions" of Notice 98-52.
In particular item 3 of that section?