Before I decided to ditch the metal tank project & proceed w/ my fiberglass tank, I was trying to remove the liner in my SuperSport tank after I put knee inserts in. The PO had sealed over rust w/ what was apparently POR-15. That stuff will never ever come out - most of the time that's a good thing, but not in my case. I also had cut out the filler neck indentation & welded in a new plate w/ a hole for an aluminum flip top cap (but hadn't sealed the cap in yet), so my situation was similar to yours. I sloshed all different types of chemicals around in the tank trying to get the stuff out.
Here's how I sealed it up: I used a rubber stopper in the petcock hole, then threaded a pipe cap on the the tube coming out of the tank. Since yours doesn't have that, I would try to put a rubber stopper in the hole & thread bolts in the other 2 holes. Then duct tape (the real aluminum duct tape worked pretty well). For the filler hole, I took the old gas cap & put it over the hole I had (no neck, so it just covered the hole) & taped it down. I left the vent hole open so that I could put a piece of tape on it while I was sloshing around, then vent it when I was letting it sit.
This wasn't leakproof, but I didn't get much nasty stuff on me or the garage floor. You might eat off some primer, but keep wiping down anything that leaks out & you should be ok. Worst case is you have to re-prime it.
Also, I would check out the FAQs. I think Bob Wessner has a pretty good write up of what he did to his tank. If I remember correctly, that's where I got the idea to use tape, but I'm not sure.
Good luck,
Jay in Philly