MB Quarts are well respected, the CDT's are supposed to have a brighter axiom-like sound and are considered a good value by most. Bostons are reputed to be laid-back, however the top line bostons are supposed to be quite different.For every brand mentioned in this thread there is someone on the fbodyaudio board that has them or used to. When auditioning speakers use a cd you know well. Don't camp out in the sweet spot, listen off-axis as you will in the car. A set of comps is not nesesarily a must-have if the install becomes a problem, a quality set of coax speakers can be very good as well. Whatever you get I would suggest 50 wpc a min. if only running 2 ch., especially without a sub.
The better comps will have adjustment switches on the crossover for slope and/or tweeter attenuation (mine are dialed back 3db,maybe 6, I forget) figure on acessing them a few times before you're happy with the sound. Some guys put them in the doors, I would try not to due to moisture, although honda doors are probably drier than most. Mine are behind the plastic trim panels over each rear wheel house. The kick panel area is the preferred location for front comps but it takes custom fabrication to do it right, and now were gettin serious. The q-logic panels are flimsy plastic and far from optimum, but may become your only option if the stock locations don't work out.
The x-over on amps is for sub integration, same as the x-over on axiom subs- you'll most likely bypass it and use the x-over in whatever head unit or processor you wind up with. Car audio amps vary in quality more that home amps but a good amp is still a good amp-Alpine is considered a pretty good value, JL Audio is a solid investment,Rockford fosgate,JBL ,beware on anything that seems too cheap or too expensive compared to the above.
Sony- 10 yrs ago sony was very good, today sony is the BOSE of car audio, run away from sony or anyone trying to sell you sony.
Subs- unless you're a serious bass head a single 8 or 10 of good quality in the right box and with good power will be all you'll need.Good power to me is 300-500 watts.Make sure to match the impedance of the sub and amp. Car subs is an entire hobby by itself and installation makes far more difference here than anywhere else.Unles you like to get quite loud I would be tempted to hold off on a sub till later and see how things sound without one. Maybe run rca's and size the power wire for that option later.
Caps are a myth- to be useful you'd have to fill the trunk with them. Unless you're gonna be "bumpin'" with your boyz for hours on end in the mall parking lot a different battery shouldn't be nesesary in my opinion, if you put a 1000w amp on a big-ass sub you may want a high output alternator or your lights may in fact dim with the music.

I'm tired- going to bed now