I'm in the identical situation: I picked up a 1995 Ibis cousin IT frame for $100, and I'm planning on taking it to Bilenky in Philadelphia next week to ask about a retrofit.
I do have experience with using Bilenky to retrofit a Bruce Gordon Rock and Roll touring frame which I found used for a very good price. Bilenky welded in a bottom bracket for the eccentric and a Rohloff dropout, in addition to brazing on S&S couplers to the frame. I got exactly the bike I wanted (Bruce wouldn't do this for me on a new frame) at substantially lower cost. The Rohloff is an incredible hub, and I'm using it with a drop bar. It gives you a range comparable most mountain bike triples. And Bilenky does beautiful work.
The only concern that I would have is the chainstay length to avoid heel clash with panniers. I haven't measured this yet and it could be reason for not doing the upgrade for loaded touring. Also, relative to "modern" framesets: if you're building this bike for loaded touring you want a stout frame that will avoid flexing side to side. The Ibis cousin IT frame seems well suited.
Regarding disc brakes, my choice is to avoid them. They cause a twist under load on the front fork if you're riding a loaded single, much less a tandem. In the rear, the disc brake creates real difficulties with fitting a rack. Go with the Paul touring cantis, which I've got on the BG and are spectacularly efficient.