Super tuning car runs good shooting for great

As for the timing variations: The ignition system ECU's (orange boxes and MSD's) have some level of internal regulation inside of them to avoid having the timing effected by small to medium voltage variations on the system. So either you have a really big voltage variation going on with the alternator hooked up, or the problem is in the grounding or sensor polarity, that is simply changing the trigger point that the module is seeing. How much total timing variation are you seeing with the alternator hooked up? What grounds do you have connected?

With the alternator hooked up and things running, what DC voltage are you measuring across the battery? And then what voltage are you measuring on the ignition module? One test that might be worthwhile is to switch the meter to AC and repeat the above measurements and see how much AC voltage is present. But if your meter's lowest AC voltage scale is 200 VAC, then this is likely not going to register anything useful.