These sort of situations are very frustrating indeed. As I read you post one of my first thoughts was like you - the voltage regulator, considering you've already taken care of the usual bad grounds, etc.
I'm with you, I don't see how the lower fuse rating could cause any issue so long as it had not blown. I recall that thread regarding the incorrect fuse installed in later X's. It still sounds very odd to me.
If your issue has resolved then I assume it was the ignition switch. If so I'd consider doing a "master relay" mod to eliminate the current through the switch, transferring it to a high quality, large amperage relay. I'm not talking about any BWM, relays to individual accessories, etc, as I know you have sorted all of that already. This is a main power relay to "bypass" the load from the ignition switch completely. I went the other route and added relays to every electrical component that can draw more than a moderate level of load, giving each component a separate power feed. But it turned out to be more than I anticipated with several new relays and a lot of rewiring (I installed all of the new relays into the existing fuse/relay box by adding more of those little factory plastic relay holders to it). If I were to do it again I think I'd go the other route and add a master relay at the ignition switch instead of most of the individual ones.
@kmead has discussed this approach in better detail before, maybe he can elaborate more.