I drive a 2006 ZX4 SE with an FSWerks Cool Flo intake as my only mod and although I don't know what my times are, I know that from 0 to the 1/4 marker, I was doing roughly 80mph when I passed it. That's not fast, but it's not dogass slow either. At least compared to slow cars.
Get a tune and you'll probably increase your times by like .3 -.7. Any mods beyond that will only help, so look over c-f-m.com and see what looks good to you.
As for dragging being bad on the tranny, I was thinking about calling my local tranny shop and asking them if there is anything they can add to my ATX to help it not take such a beating.