As far as the mids and highs go, I'd set the HPF at about 100 hz, and that's it. Set your gains with a DD-1 (best), an oscilloscope (good), or digital multimeter (better than nothing). There are videos on YouTube that will teach you how.
I'm not going to tell you to get rid of the caps, but I've never had good luck with them.
I would just keep the subs flush personally, but you can invert them and see which sound you like better. If you invert them, just make sure you wire them 180 degrees out of phase.
I'm not quite following how you wired the subs. Are you connecting both subs to a single quick connect? Or does each woofer have its own?