When I got a custom seat made by Bill Mayer Saddles, I asked them to raise the seat height, both for the comfort of my legs and in order to be able to add more foam for my butt. It helped my leg comfort quite a bit.
I notice they have a custom seat that you can add on top of your regular saddle, and that it comes in low, medium and tall profiles.
http://billmayer-saddles.com/ergo/You might want to give them a call and chat with "Rocky" (Bill Mayer). Most likely he will remember my bike, its seat pan with its weird rise (to accommodate the charger), and will have some ideas for you.
Another cheaper solution (but probably not as comfortable) is an AirHawk air cushion.
http://www.airhawk.net/airhawk-r.aspxI tried one, but didn't like the lack of stability. It felt "squirmy."
Lowering the pegs would keep your overall center of gravity lower, but at the expense of less clearance in the corners.