Thanks for the input Chris. I haven't done a good job of keeping this thread up to date, so here's the latest.
Turns out, I had a combination of problems. At some point in the past, someone had used a punch or screwdriver to adjust the chain. This buggered some of the notches in the eccentric, and those were dragging and catching on the swing arm. I WD-40ed the eccentric and worked it back and forth and was able to get more travel out of the adjuster. Unfortunately, the movement was only in the "loosening" direction.
So I bit the bullet and bought a 41mm socket ($35, ouch!) and took the whole works apart. It was surprisingly clean and in good shape, other than the damaged adjuster notches. I filed those smooth and put it partially together. What I found is that there's a slot in the brake caliper bracket that rides on a pin in the swing arm. The slot isn't long enough to allow complete rotation of the eccentric as Chris mentioned. As a temporary solution, I'm going to remove a link from my chain, but I think I'll need to replace it in the near future. It's a 103 link and the rear sprocket is a 41 tooth, both of which I believe are the stock sizes. I think I can measure links to determine if the chain is out of spec, so that's on my to do list.
Also, I was able to finish tuning the injection over the weekend. Starts right up and idles nicely. It's cold and rainy/snowy here, so I haven't been able to take it for a test ride, but I think I'm really close. Now I just need the weather to break...
Breaddrink, I put a couple of pics in post #3 of this thread. Not much has changed visually since then other than a pair of bar end mirrors (one of the originals had a crack).
Thanks again fellas.
'06 Ducati S2R1000, '06 Ducati ST3s
'00 Yamaha WR400, '03 Honda TRX300ex