Well, I thought I should get my butt in gear and do a build update post, since this thread has been getting more views.
One issue with a bed bob on a Taco is that the exhaust sort of hops over the rear axle and then spits out the rear. By eliminating some bed length and swapping to a boxed frame section at the very rear (Hilux), you lose an exhaust hanger and sort of lose the reason for the exhaust to hop over the axle in the first place. We decided to do a side exhaust, which will have its own little skid that will continue back from the slider (to be fabricated next week). This also reduces the total exhaust length and mass that will be bouncing around on unpaved roads.
In the process, we did NOT drill or punch the frame, and were able to replace the ridiculously huge Toyota muffler with something more reasonable, making some space.
You'll notice in earlier pictures the driver's side (left) bed was not shortened yet, but the right was (look back at these pics for a comparison of the two bed lengths). Now, the left side matches the right.