I did the same thing a few years ago - did a "headectomy" on my '85 JJT to get rid of the smell, complication and maintenance. I did not cut the top out of the tank but worked via the existing round hatch. I flushed the tank with water, then filled it with water and bleach but can't recall what mix or for how long now, but the weaker the solution the less risk of doing damage, just leave it longer (I think I went with 100:1 and left it for a couple of weeks while I was away). After pumping out the water I let it sit open for the rest of the summer and all winter as drying will kill a lot of cooties. Then in the spring I put on heavy rubber gloves and took an old, long handled barbeque scraper and reached back in the tank (face to floor, arm all the way in to the shoulder) to scrape out what was left of the (hopefully) inert dry sludge clinging back there, and there was some. Then I repeated the bleach and water drill and wiped it out until all rags came out as clean as when they went in and let it dry again, and left it sit open for another winter. I am satisfied that it is clean enough to use for other purposes now. Probably could have been done a lot sooner if I had a steam cleaner but that may not have looked after the sludge. Like Dave, I haven't decided what else to store in there, though with the slope to it I think it would make a great stash for bottled water or beer as each time you take one out, another will roll down into it's place - a gravity fed vending machine. I've experimented with wine bottles and they stay reasonably cool. As for leaching into the hull, the tank is lined with epoxy paint by the look of it, so I don't think I'd worry about the contents seeping into the hull.
As for the other part of the project, I too acquired a small port-a-potty. As I am a solo sailor I also use bags that hikers use for "pack everything out" situations and simply chuck them out when I get to shore. Operating marine heads really don't make much sense on small boats like ours, but the problem is people who are irresponsible with their waste, especially in closed water systems like lakes. Having said that, if you choose to go "headless", you may be contravening the law. I also understand that some sailors and/or their crew won't go without a toilet, so I dare say that's part of the decision making process.