While I'm out of town, I finished up my research by posting a cry for help on VAF and getting relatively consistent answers, but nothing concrete. I then wrote to Van's and asked point-blank:
Subject: Re: identification of nutplates
From: David Hill <email@example.com>
Date sent: Tue, 9 Jul 2013 11:07:29 -0500
To: "firstname.lastname@example.org" <email@example.com>
I've made new bins for everything, but I'm still not sure which is
which. Is an -06 smaller or larger than a -3?
A # 6 screw is quite a bit smaller than an AN3 bolt, so the threaded opening on a K1000-06 is
smaller than the one on a K1000-3. The rivet holes will be the same.
If you're not familiar with basic sizes of screws (#6, #8, etc.) you'll have to learn them. Then
there's number drills and decimal fractions, along with imperial fractions. It will make you
seriously yearn for the metric system...
Well, I do seriously yearn for the metric system, but this event really rivets my attention on the matter. (Sorry—couldn't resist.) I've clearly screwed up and placed K1000-06 nut plates instead of K1000-3's. When I get home, I will have about 150 rivets to drill out.
Oh, well. This project is all about learning and being an expert de-riveter is a skill, too!
Further perusal of VAF describes using a small nail (or an old mandrel?) to punch out the steel mandrel remnant in the rivet to be drilled out, then using a slightly smaller drill than the original hole calls for (e.g., a 32 or 33 vs. a 30) and possibly a pair of diagonal cutters to prevent the rivet from spinning. I'll let you know how it goes.