Sometimes should be an exception brother. All Civic models, Margalla, Baleno, the lot do touch sometimes.
What kind of springs do you have at the front? I don't think they are genuine ones, or have you installed spacers etc?
New or old, dampers do not effect ride height at all. Your coil springs and rubber bushes do.
I'd suggest you to get rid of the spacers, if there are any, and install genuine springs at the front and slightly stiffer ones at the back. Try to find something like Tokico or other reliable brand, do study and compare their spring rate online- or get one from an Integra, that's not possible, is it?
I'd go even for good quality, local made ones for the back end- chose ones with the same wire thickness but an extra couple of coils- do not go for macho wire springs of any sort.
For the resonator, try to change its rubber mounts, if the resonator itself is OEM. Saggy, old mounts do cause problems like the one you're facing.
P.S. Can someone here tell me how'd changing to bigger rim size help?