Not sure if you have a chip or not, but if you do you could make an auto boot game and load it using the savemiifree method. On this disc can be a modified app that uses GC pads.
Now the app would need to be one of the many out there that can update/downgrade or change the sys menu. This in theory would remove preloader and once you boot the wii it would go to a sys menu and you could then resync your wiimotes.
Sorry for the "sketchy" info only had a few minutes free to scratch my head on this one, or you could try what I suggested in irc and hunt crediar down and ask him maybe.
Hope you get sorted.