After finally finishing the drilling and tapping of the slats, I moved on to the trusses. My plan was to make a jig to drill all of the screw holes, then flip the truss over, and use a larger bit to drill the "access" holes.
Here's the simple jig I came up with for the screw holes. It's basically the same ideal as a shelf-pin jig, as you might find in woodworking. The idea is that you drill your first hole, then drop the jig's pin (the machine screw in the pic) into that first hole to locate the next 2 holes. Then rinse/repeat all the way down the length of the truss, keeping the spacings consistent, and thus hopefully well-aligned with the tapped holes in the slats.
I knew my alignment wouldn't be perfect, so I did drill the screw holes to be about 1/16" oversized. I'll use washers under the screw heads, so a little slop in there should be ok.
Next I flipped the trusses over to drill the access holes. These holes need to be large enough for me to pass the screw and washer through to the screw hole on the other side. They don't have to be perfectly aligned, so for this I just used visual markings to get the spacings right; this let me go a little faster for this part of the job.
-Jake