Thank you for the compliments on the write-up. I apologize for not looking at the thread for a while. It seemed get lost in newer threads and the mountain of work at school.
I thought about the capacitor. I wanted to run the setup without one and determine later if I needed one. The extra money was not worth it to me up front. So far, I've made the correct decision. No problems yet with batteries, alternators, etc. As for the seat clearance--it's minimal. The seat will latch down and rest with about about an inch of clearance in the front and very little, if any, in the rear. Though this seems close, I have not had any issues with overheating. The amps stay cool and dry.
As far as 6x9's, speaker bars, and amps are concerned, a lot has to do with the manufacturer and the components. If all the pieces match and are fit for each other, the setup will work well. Sound bars are fine if you're willing to spend the money or have a connection to one. Personally, I enjoy building the components. I have the 6x9's in the rear and they are amplified. They sound nice but are a bit "barky." Just ensure that your amp can provide the correct power amount (RMS) that your speakers are specified to handle.
1990 Red YJ 2.54 L (Rebuilt) 5 Speed with 94 rollbar | Dynomax Exhaust | Luk Clutch
2.5" Old Man Emu over 31x10.50 BFG MTs on 15x8 AR 767s | 1" Daystar Body Lift
Two Tops | Full and Half Doors | KC Daylighters | Hella 5500 | OME Steering Stabiliser
Sony CDX-GT300 | Kicker ZX500.1 | Kicker ZX350.4 | Kicker ZX200.2 | Kicker L5 Solobaric Sub | Kicker 6x9's | Apline 6.5's | Boston 4x6's
Truckstop CB Antenna | Class 3 Hitch