Those V&H pipes...are they slip ons using the FB headers? Is it the mufflers or headers that are dragging?
I always wondered why all the Softail bikes had those up stepped headers. It seemed like a good idea to get mufflers up so they wouldn't drag. I think they look cool too. Best of both worlds to me. At one time I was scheming on getting a nice set of ST take offs and fabricating new mounts to use them on my FXR4. The V&H HotShot (2into2 slash cut megaphones) pipes on my bike drag way too easily for my taste. However I decided to just make new mounting brackets to get the lower muffler up and in a bit. These days I'm thinking the step up on the ST pipes was designed that way to mainly keep the muffs from dragging since ST bikes are so low to begin with. If your pipes don't have that step up at the header you might have a hard time getting things to clear. You're right in wanting to get more height. I would look to larger diameter tires to help along with any rear suspension mods you come up with.
As far as the Jiffy stand dragging goes, well, to me it's just a poor design by Harley. Mine drags too if I lean it over far enough although, of all the things that can drag, the jiffy stand is the last to drag.
Harleys.....! Owning one is often what it would be like to be married to Lindsay Lohan. Looks good and fun at times but can have a heavy maintenance price to pay.