Are you sure you only have two pinholes?
Unless the holes are from impact damage or some other mechanical cause, then the holes came from rust, and if it rusted THERE then it probably rusted elsewhere also, maybe not enough to go all the way through, but my point is: how thin is the metal in that area now?
If you're pretty confident that there's really only two holes and the metal is sound, why not weld them up? That's a trivial job with a welder, and no worries about crapping up your fuel system. (naturally drain rinse and purge the tank before welding)
If the metal is sound and you can't get it welded up, then after making sure the metal isn't dangerously thin in that area I would apply a small amount of standard two-part epoxy from the outside to close the holes, AND then line it with your liner of choice. The epoxy from the outside is just to make the internal liner lay down nicely, if just used alone without an internal liner, it would be destined to fail.
All in all though my personal preference is not to line tanks, so get it welded up if possible. If they're literally pinholes, then you're talking about 5 seconds of actual welding trigger time, with time for prep and cleanup on either side.
BTW if it were me, before I did any lining, I'd also take the tank, seal up the fill hole, run a small amount of air pressure into the petcock hole, and immerse the tank in water. Don't rely on visual inspection if you're dealing with pinholes, a bubble test will reveal them for sure. Mark them by circling with a scribe, then dry off the tank and plug them by welding or with epoxy as per above. Then you can repeat the test until you're 100% sure the tank is airtight. THEN worry about the internal liner.
mystic_1