With 2 sets of nuts and bolts, how do you keep it perpendicular (or maybe even 90°). 

I assume you need to tighten those nuts... spanner?  Gotta be an easier way if I'm on the right track...

Shame about the issues.  Haven't the Incra TS, but the router and hate to see it go to waste.

If your first cut is too short... Take the second cut from the longer end... LBD