You could try Red-kote I had luck with it on a rusty dirty tank on a Honda. Took some BB's and drop them in and shook the crap out of it for several hour over a couple of day. That seemed to clean it pretty good, then just follow the directions. My buddy is still riding the bike today.
Haven't used that one before but have a couple others. Honestly my biggest concerns with any are the prep/cleaning and, of course, just protecting the outside.
All the currently loose areas are actually less of a concern. Some type of abrasive in the tank and moved around will break all that off. It's the remainder that might not be as clean and would likely continue to do as this has done. I dread the idea of this problem continuing even if it was doing so under some new outer internal coating. I just don't trust that with any home bench method I might come up that I could completely clean the inside while concurrently not damage the outside.
More homework is obviously in order.
Just read a PM from another site member recommending this service provider:
http://www.fueltanklinings.com/Spoke with the gentleman on the phone. Man, what a talker; in a good way. Professes to be the source that Harley recommends its dealers to send old tanks to along with doing tank service on everything from Ducati to Farmall. Neither a quick nor an inexpensive service. Described a "process" that could take three weeks or so and would cost about $600.
No idea what the man hours or EPA requirements/costs might be so no idea if the cost is fair from the perspective. Compared to repainting an otherwise unobtainable tank the cost is definitely ok though. Best thing he said though is they do whatever it is they do with no harm to the exterior surface while the interior is completely stripped and re-coated with something as magical as Pheobe Cates undergarments (my words not his).
In doing a little online homework on this since first seeing the problem while I'd not seen many offering a solution I did find a few references to others having this problem. Apparently less common in more recent years but more so over the years that would cover my old bike.
So; anyone know about or have experience with the provider mentioned here? So far he's the only servicer I've stumbled in to that offers a service that specifically does what I'd most like done; completely stripping and re-coating the inside without harm to the outside. Oh yeah, and the work comes with a "lifetime" warranty.