Well looking at your pipe I see two things I would prolly do if it were mine and I think done/approached neatly it will not hurt aesthetics . The section where the pipe comes right next to and close to the front down tube. I would fab a Muffler U bolt bracket. Now I hate the way U bolts will ride and leave a crease in bike tubing. So I would get a piece of fairly wide strap steel use a table vise, Map gas torch, and a piece of similar size pipe [shaping purpose to match the down tube] Then weld that preshaped section of strap steel inside the Muffler U bolt set up.
Take some Leather or old tire tubing put that between the down tube and the clamp. Mebbe make one more similar clamp by the seat as well? A good muffler mounted further back may prove to rattle too much? As for putting a nice quite Muffler on this pig mebbe run larger diameter pipe off the rear of the tuned pipe to help aid in gas exhaust expansion exiting the tuned pipe.
Stub off old old pipe OD. at mebbe 3 inches? Put new larger freely breathing OD. pipe over it all flush to the rear exp pipe cone? This would let you mount a nice quite muffler further back on the bike me thinks and still have the motor perform and breath freely.
These are just my thoughts having been familiar with this pipe on my own 5.8. build. I like every thing to be solid as all possible with my installs. No rattling of any kind so I do tend to go a little over kill.
Then I don't ever have to mess with it again. That pin hole leak will seal up easy enough with a spot weld Mig or brass brazing.
The carb you got that float is not adjustable. I got a thought that mebbe dunno? The extra weight volume from the large gas tank may be challenging the the float needle assembly to control flow Dunno? I saw in the pict what looked like light wet dew around the float bowl.
Dave3 found a nice foam air filter might P.M. him it fits his 5.8 carb nicely. I think it would give and contour at your frame nice enough? Theres another alternative a ho-made filter/air box with mebbe just a couple layer of black nylon stocking stretched over it?
http://motorbicycling.com/attachments/f47/18326d1262410605-dave31-scsw-boxer-sany0747.jpg