Chances are the old aluminum gasket is now clogging up the inlet into the muffler, so take the muffler off and make certain you get it all out.
Might be the cause of the leak at the front end too.
Opening the inlet into the muffler out a little doesnt seem to harm much either - the small hole in the centre can be opened out to 1/2 " or so which will add a pleasing burble to the exhaust note and will sound a bit faster.
I tried aluminum flashing for the gasket but withing a couple of months it had vanished up the exhaust and was melted into a solid blob and blocking the muffler inlet again - I would just shell out the $13- and do the job properly.
Adelaide Hills, Australia. 93 R100 GS, 77 R75/7 ,70 BSA B44VS, , 86 R80 G/S PD, 95 BMW Funduro F650 ST