PLEASE, get someone who KNOWS Model A's, to help you wire all systems to stock & it will work.
We can't help you much, in your confusion, when we can't see & touch & test stuff to find/correct the problems.
Off hand I think something is screwed up from whatever NU-Rex stuff you had wired up in the car.
STUDY, STUDY, STUDY, the original wiring diagram & hook up stuff accordingly! Excluding the lighting system, Model A wiring is about as simple as it gets. About the ONLY odd thing is that the ignition switch turns the current off/on, between the coil & the distributor, unlike most other cars.
Sorry if I tipe "stern", I gotta' go pee!----Bill W.