My tip for that 3rd starter bolt? Don't reinstall it.
I've run for quite a while with just the two lower bolts; works fine - the nose cone of the starter is a slip-fit into the bell housing spacer, and as long as the starter is kept from falling out, that slip fit will take the twisting force.
Anyway... that's what I've done on all those short starters because it's such a pain.
On the longer style(Mitsubishi?) I can usually get the 3rd bolt without too much hassle, but I've left it off for expedience before as well.
I've also run a two-bolt starter that used the top and bottom-most bolt with plenty of clearance on both. That was nice.
(it was off of something else, marked 'cummins'. Not a 5.9 though)