So uhm, what's the potential downsides of running a wider shock bushing than the stock lower shock bolt?

I've got Toyota FJ60 front shocks in the rear of the GV and the bolt they intend for you to use is several milimeters (say, 2mm or so) wider than the stock bolt.  I couldn't find anything to make it work and couldn't get the bushings out of the stock shocks for the life of me.  I ran out of time so just slapped the stock bolts in there and so far, so good.  No funny noises, it rides fine, and the wife hasn't mentioned anything.

You stand a chance of wearing through your bushing.  It probably isn't a problem, but I would check it after a few weeks to make sure. 

when I put my pro comp shocks in I just did the top bushings way tight and they didn't bind. when I added my spacers to let it sit properly for the longer shocks I put in some poly bushings I got for free really tight and it flexes great. if you get those top bushings too loose you'll probably develop a gap there when you flex like my stock ones did.