my advice is go with 16 inch rims and tires...or even 15 inch rims and tires. Civics were not meant to have 17 inch rims. the more "tire" ...the more cushioning. upgrade your suspension parts with quality parts. you get what you payed for. 3.25 inch drops were meant for show...on street/daily driving, it is ridiculous. your stock shocks have no travel on such a drop. this is only my advice. its your car...you dont have to take it.
if you decide to keep your setup the way it is...best way to go is to get sport shocks such as the Koni Sport (yellow) which can allow extreme drops such as yours with the adjustable perches to allow for better piston travel. this way you wont be "bottoming out" as much.