Howie pretty much covered it.
1. I have not personally used either of these units. I hear that both brands are OK.
Do keep one thing in mind: A. Most manufacturers don't/won't provide tech support on their phone lines if you're a do-it-yourselfer. B. The more popular the brand, the more of us on the forum who can help you if you have a problem. So basically, even if you have to pay, say $25 more for a popular brand, the free tech support you'll get here on this site will be worth it.
I use Audiovox all the time, and anything from DEI is very popular and pretty much any installer has worked with it before. The Prestige APS997C is a solid unit at a good price, although the 2-way remote is very fragile.
2. Does your existing remote have a trunk button on it? If not, then you'll have to install a trunk-release motor on the inside of the trunk lid. It's basically a cable you attach to the car's trunk mechanism, and the motor "yanks" the cable. Very primitive, crude, and unreliable, but the part is cheap.
Basically, what it comes down to is if you're patient enough to keep repositioning and readjusting the thing until you get it working right.
3. I think the most popular window module is the DEI 530T. Each piece does two windows; if your car is a sedan, buy two. Be aware that you have to fish wires into the driver's door.
4. Not sure of where you might find pics besides a Civic forum, but your car is so simple, it's easy to look under the dash without tools. The panel in front of the driver's knees comes right off by just twisting the two retaining tabs. The black panel above your feet comes off the same way. You'll see there's plenty of room to access the wires going to the ignition switch, you can plainly see the doorlock wires where they pass into the body from the driver's door, you can see the brake pedal switch, and you should even bee able to see the (unused, taped-up with blue tape) light-green factory alarm connector.
The downside is that any alarm you install will be easy for the thieves to reach up and unplug. Like Howie said, you could remove the instrument cluster and hide the main brain there, then drop your wires down to where you'll connect them..... but generally, trying to hide stuff will become very time-consuming for a first-timer.
Maybe you'll want to try doing a "basic" installation in your girlfriend's car, then try hiding everything in your own car after you've had some experience.
5. Aftermarket stereo shouldn't change anything. Only one thing might be if there are amplifiers or subwoofers installed, you may find that the installer ran all those RCA and speaker wires across the place where you're about to do your work. If so, no big deal---just leave them alone, but make sure to zip-tie them back up when you're done so they won't fall on your feet.
P.S. You didn't mention this, but be aware that your car has an anti-theft immobilizer chip in the key. The remote starter won't work all by itself; you'll have to also deal with the Civic's immobilizer. Fortin's HONDA-SL3 is your most cost-effective part, but look around for others. The DEI 556U will save you money, but you'll give up one of your existing keys.