I made 3 variations of the jig for drilling the bolt holes in both the ends of the stretchers and into the side assemblies. The first one was just to be able to mark where the holes would be drilled, with the plan to use a combination of drill press, hand drill, and dowel drilling jig to drill the holes.  I came to my senses and realized it would be much simpler to drill the holes with a plunge router.  The second jig was like the first, but with the holes enlarged for a 7/16 guide bushing.  Unfortunately, the jig wasn't stable enough with the router setting on top of it - too easy to rock it back and forth, so I scrapped that one too. The third jig was like the second but lengthened so that it could rest solidly on the surface of the MFT. 

Here's the full set.

This was an attempt to use the second jig, but even with additional bracing clamped to the stretcher, it was still too unstable.

The third worked better after I figured out I needed to shim the side rail on the MFT to get a right angle with the top.

The result after plunge drilling a 1/4" hole as far as possible.  I hand-drilled the remainder of the required depth into the stretcher.

For locating the jig on the side assemblies, I used a sacrificial short piece of tenon in each of the existing mortises to locate the jig.

I used the drill press with depth stop to drill the holes for the dowel nuts in the stretchers.

I used flat head bolts with countersunk washers:

With the bolt holes in the side assembly drilled all the way through, I drilled the outside screw head counterbores on the drill press.

I had a legit sit test afterward with the chair assembled and taken out to the deck.

There's only a few things left to complete before I do the final edge roundovers and sanding: the arms and the pillow support rail and its mating channels.