I've done the upgrade on my bike and just did the upgrade last week on my friend's ST. We built our own toolkit for his upgrade. Eventually we found a perfectly sized drill bit for the gear alignment and we cut the butt of it off, drilled a hole in it for the cable, and made a perfect replica of the Lewis pin. It took us several tries to get it right, and the one time it really sucked because we got the alternator in, the pin out, but the stinking pin wouldn't come out through the oil drain hole!
I wouldn't bother pulling the pan, it won't help you that much. Put the gears in separate of the alternator and you'll know once you get the base seated enough to continue to put the alternator in. You shouldn't see the o-ring. It sounds like you just need to fiddle with it a while. It took me 5 or 6 times scratching my head wondering why the base/gears wouldn't go in this time when all I had to do was keep trying.