Steve,
I am guessing with this answer: the Factory Assembly Manual has a poor picture of the side-mount spare tire assemblies (Section 10; Sheets 3.00-3.01). I think that the two bolts through the top of the frame rail and the two bolts through the bed side (above the floor) are flatish-domed phillips-head bolts.
This is the way they came on the three assemblies that I have worked with (who know if they were original-style bolts by the time I got them).
Tim