Muffler mender is similar to JB Weld (cold-weld type of compound, but handles heat pretty well). There are several different brands, all are about the same. You can find it at most auto parts stores. That's the only thing I can think of that would seal up a leak (that is easy to use for the do-it-your-self-er) where the slip-on connects to the head pipe.
Glad to head your happy with the pipes; yep, plugs should look good with just a pipe change out if you haven't modified/changedthe airbox. If the plugs are getting a light brown to them, that usually means you are right on with your jetting/AF ratio.
Are you getting a lot of decel "popping." If not (some people don't), then you don't really have to mess with the PAIR system. But, most that take it out of the equation usually notice a better sound (and usually louder) from their pipes. Yes, you can just "disable" the pair valve. Look on www.vtxoa.com
and do a search in the 1300 tech tips section, should be able to find it pretty easily. But, to disbable it you have to remove the tank anyway to get to the lines for the reed valves (on top of the cylinder heads). My philosophy-spend the $13-20 for the reed valve block-off plates and take the whole mess out of there. The one thing I've read that you have to worry about just disabling it (which is basically just plugging the lines with bolts or vacuum seal caps) is a leak and build-up of condensation/moisture in the system, which is never good and can find it's way into other areas of the engine, etc. Basically, if you're not using it, why keep it on the bike? Just a thought.
Good luck, let us know if you have any other questions.