The next size up would be a 5/16 liner, that would move your drilled hole up by 1/32 of an inch, plus a little for the chamfer. Will that work or is that going to go too far?
Here is what may have happened - i think you said you got the countersink from Track, was it one of those single flute 1/4" type? I think you know by now you ran it too deep - man don't think I'm giving you a hard time, just trying to help you figure this out,all of us here have made mistakes and know what it's like. Even if you ran the countersink in clear past the cutter, the shaft on one of their 1/4" size is only .250 wide, the hole you'd drill for a 5/16 liner would measure .272 and should clean out the old threads and open up the previous hole. Check your countersink and see if it's like what I'm talking about.
If you absolutely can't move the top edge of the liner up that much - you mentioned that your vent was a bit higher than the top edge of the pan, this may end up helping you. If you know of somebody with a milling machine and they know how to use it, they ought to be able to open the hole up to the next size while moving the center of it down toward the pan.
Welding it up and re- drilling was mentioned and would work.
However you do it, make sure when you countersink for the new liner, all you need to do is break the edge, real shallow, all this is for is to make a place for the shoulder to seat against when you tighten the liner down.