I never noticed that the V&H was so low on the right side. On mine, the transmission bash plate is still the lowest point of the bike.
I stretched the collector on the right side 3 inches so it would cross-under in the correct spot and I could use the stock cross-under bracket. It normally connects to the transmission pan but I made an adapter setup to connect it to the engine portion of the rear isolator (engine mount). In this picture you can see where it exits on the left side. Leveling the left pipe in relation to the saddlebags was critical to a stock look.
I originally suspended the mufflers from the saddlebags but was wearing out the rubber isolators too quickly. I connected them as a test using short Pitman arms but it started transmitting vibrations into the bike. I then committed myself to making a bracket that would support the entire exhaust system from the engine assembly.
The bracket worked fine and allowed me to ride without the saddlebags if I wished. I was adding fishtails to the mufflers and since I would need clamps, I used this opportunity to stiffen up the left muffler by running a polished aluminum tube between them. This was what was finally need to create a complete "box" to the exhaust system. I could probably get a few guys and lift the bike off the ground by the mufflers if I wanted to. No vibrations from the exhaust and I have done two cross-country trips without a concern from the exhaust.
One thing that I have noticed lately, almost no one will ask about my bike for fear of sounding ignorant of old bikes. They stare but will not ask questions.