Hello greenpilot, If I can picture your description correctly, something is not normal with the fitting of these parts and / or, the length of the bolt and/or, it's thread length.
To answer your question about Loktite between the parts.... I guess you could dab some on there.... BUT that will not be the solution to this problem. Do the muffler parts EVER get tight OR do they work themselves loose? It just seems that the bolt and nut that ties the two pieces together may be the problem. What I am saying is... the nut may "SEEM" to get tight. Is it possible that it has "runs out of treads" and the nut can't go any further?? (THUS leaving the muffler parts still slightly loose) Try to add a couple more washers as spacers if this is the case. You can take the baffle out (?), but that again I feel is not going to solve the problem. (not sure how it fits in your muffler..but it could actually increase the problem if it makes the total length of the muffler shorter in length. Now your bolt may not tighten it at all.
Keep us posted..... I would like to know what is going on here.

PS. When using the LOKTITE, be sure to clean the parts first with alcohol or acetone etc. Also... some types Loktite is meant to "creep in" the threads, and some has to be applied. (check the directions)

....lownslo....

Bob