
The technique I ended up using with the tool is the most brute-force method, but it ended up being the fastest (albeit incredibly tiring). Basically, I took one hole in the scrap and drilled the nutplate rivet holes next to it. Then, for each hole I needed to countersink, I followed a 3-step process:
1. Cleco the alignment tool to the spar flange, using the rivet holes adjacent to the hole you're countersinking.

2. Place clamps around the clecos.

3. Remove the clecos. Now the alignment tool is clamped in place (make damned well sure it won't slip). Now you can countersink the hole. If you're asking why the hell I didn't just leave the clecos in, it's because the microstop is wider than the space in between them...just doesn't work out. I read somewhere about a builder clecoing up from underneath, and then cutting two notches in the microstop so it "straddles" the cleco ends, but that's way overkill in my opinion. So, in the end, this cleco-clamp-uncleco-countersink-unclamp process worked great. But after an hour my hands were tired, to say the least.

This process worked so well that I actually flipped the spar over and redid the countersinks that I made last night (that were crappy anyway). Just a mil or two deeper and MUCH, much cleaner. Centered up and smooth. Glad I went conservative last night...it left room to clean up today.
The left wing countersinking took about an hour. It "flew by" relatively speaking. Again, very tiring, very repetitive work.
After deburring the holes I went ahead and countersunk the rivet holes. That was a no-brainer and way quicker by comparison (thank goodness).
Hey, by the way, the white strip you see here is masking tape. I put that on both sides of each spar since little shavings like to wedge themselves down into the joint...never to be retrieved. I figure that's just asking for corrosion, so I masked off the crack. I've seen tools dedicated to this purpose, called something like "shaving scrapers" or whatever, but that's lame. If you had to, you could brush/blow the shavings out with some diligence, but I figure it's better to avoid the problem in the first place.

On the topic of shavings, just countersinking all these little holes has produced a mountain of shavings. I hear about people building in their living rooms, and I just cringe at the thought of all the aluminum getting permanently embedded into their carpet! To each his own, I guess. Or maybe I'm just lucky to have a garage. Whatever.
Here are the nutplates and AN426AD3-4 rivets.

The diagonally oriented nutplates (which straddle the wing walk reinforcement ribs) were the toughest to rivet, although this is not rocket science. Here's the left spar with most of the underside nutplates attached.

The process I used was:

By 11pm, I had finished riveting all the nutplates to the underside of the left wing spar. So I'm 1/4 of the way through that process.
Let me just take a minute to talk about how many freaking holes there are in this kit...or better yet, let's just look at the tank attachment holes. You've got 30 screw holes on each side of each spar. Each screw hole is straddled by 2 rivet holes. So that's 180 holes per wing, or 360 holes total that need to be countersunk. Don't forget to debur them (I had to drill out the 3/32" rivet holes in order for the c-sink pilot to fit...they were only "pre-punched"...whatever that means). Lots of holes. And that's just the freakin' tank attachments. Holy holes!