Lowering 2004 Civic EX
 

I have a 2004 Civic EX stock height, I just put some 17 inch rims and tires are 215/45r17 I plan on lowering it what would be a good height to lower without it messing up the tires or my car wheel well.

We can't say if lowering your car will cause your tires to rub or contact with the body. The reason some people have rubbing issues is mainly because they have the incorrect offset for their wheels. Find out if your offset is ok. If it is, you could potentially go really low without any rubbing issues.

17x7 and it has a 40mm offset

You should be able to get pretty low without any rubbing issues. 7" wide with +40 is a good offset that shouldn't rub on the inside wheel well or fender.

Search some forums and member pictures and see what people are using for suspension. Do some research on how suspension works and figure out what you want out of your suspension that fits your budget. A mild drop, around 1.5-2" with most lowering springs and a good set of shocks will provide a relatively smooth ride and slightly better performance.