YES it's very much worth it to get a wiring harness for the head unit! It'll make your install so much easier and a lot easier to put stuff back to stock if you sell the car or put the aftermarket deck in another car. We charge $15.99 for them but that's way overpriced to be honest
. I bet you could find them for under 10 bucks somewhere online.
I like the setup man, that sounds awesome! Amazing head unit, amazing sub, amazing speakers! I wish I had that kind of money.
Anyways, lemme see if I can answer some of your questions.
For the remote wires, yes it's fine to connect two amps (not more than that though) to one turn-on wire. Just run one wire throughout the vehicle til you get to wherever the amps are, then just split the wire to each amp. Obviously you're gonna do the same thing for the amp's power cable (hopefully 2 or 4 gauge.) So wherever you put your cap and distro. block, you can split the remote wire near that. if you're looking for a clean install, then I'd definitely recommend using a distro. block for the ground, too. Whateer you do, make sure the gauge of the ground wire is AT LEAST as big as the main power cable.
Since you're obviously going for a really good setup I'd run the remote wire with the power cable, down one side of the vehicle. Get yourself some good RCAs for amps (at least good ones for the 4-channel amp) and run a,ll the RCAs down the side of the car opposite the power cable, to avoid any interference/noise issues.
If you're gonna be mounting the amps on the seatback, keep a couple things in mind. If there is a center armrest which I doubt there is, but if there is you wanna make sure not to drill through the middle of the seat. Also remember that they may fit on the seatback with the seat folded down, but once you put the seat back into its normal position you're gonna lose a bunch of space on the sides as the trunk opening is more narrow than the entire seatback width.
To give it a clean look, I'd run all the wires down the sides of the vehicle, til you get to the seat, then run them around the outer edge of the seat, and then inwards towards the center of the seatback. Usually what I do is group similar wires together and put some zip ties on them, right near the edge of the seat. Then get a sharp utility knife and make a 1-2 inch slit in the carpeting on the seatback, wherever the amp's wires are gonna be hooked up. This way, the wires will be hidden except for where they plug in to the amp. You might also want to wire tie the bundles right before they plug in to the amp.
As far as caps are concerned, pretty much the only thing we sell is rockford and monster and I've never had any problems with either brand, or any cap I've come across for that matter. As far as I know a cap is a cap (BTW did you know it only costs them like 5 bucks to make a cap? talk about markup!). Just make sure not to strip the terminal threads as many manufacturer's warranties do not cover stripped terminal threads.
Technically you'd be best off running new speaker wire from the 4-channel amp to each speaker/crossover, but sometimes this can be quite a bit of work. On some vehicles it is close to impossible to run new speaker wire through the rubber boot between the door jamb and the door, but I don't think you'd run into too much trouble with your car. Some may debate the value of this but I think if you're going for really good sound you might as well do it the right way, the first time. For the speakers I'd go with 16-gauge wire, and for the sub use 12-gauge. I've never had a problem running speaker wires near the power cables but just to be safe, whenever possible run them with the RCAs.