I finally got back to the rear VS spar...I aligned and drilled the clip T12-06 and the replacement part T10-05. This time I left the spacer out and was able to align and drill T10-05 very well. I continued to updrill without the spacer, since the alignment for the spacer does not seem to be critical (since it gets removed during assembly), while the other parts' alignments are critical.
I finished updrilling the spar, to 1/8" in the case of the rivet location, and to 3/16" for the bolt holes on the lower half of the spar. I test-fitted one of the bolts and it's too tight to fit, so I'm going to updrill again using a #12 drill bit, and a #11 if I really need to. This was recommended by Sonex if the fit is too tight.
I'll deburr everything first to make sure there are no burrs causing the bolts not to fit, then worry about updrilling as described.