The weakest link in any H-D bagger's cornering prowess is the floorboards. I scraped them on my '02 Classic and I scrape them on my SEEG, though it seems to be less often on the SEEG. While these bikes are an inch lower than their non-CVO counterparts, the floorboards on the SEEGs are narrower and the mounting brackets are shaped differently (it was the mounting brackets that I ground down on the '02) which both work to make up for the lowering when it comes to maximum lean angle. As far as handling, I think the lowered shocks make for a much better-handling bike vs. a stock FLHT because the center of gravity is lower, plus the stiffer ride serves up more confidence in turns as well as on the high-speed straights, IMHO.
Regarding comfort, the two biggies have already been mentioned: windshield and seat (and in that order). For windshields, I have the 9 1/2 inch lightly smoked H-D piece which I think is perfect because it still keeps the bike looking low, but offers excellent wind protection. I liked the stock SEEG seat just fine, myself but had to switch to something my wife could be happy with, so I went with the Road King Comfort Stitch seat and have no regrets.