I used to do car stereo competitions, hence why I am partially deaf now, but here is my take:
1. Mounting the amp in an ammo can can cause overheating issues for larger amps IF you run it really loud all the time. Otherwise, not an issue. However, when someone breaks into your truck, it's going to make it very easy to steal. Yank on that box and I bet the metal can be broken easily.
I would suggest mounting it somewhere else, perhaps under the seat or dash (depending on the size). The other spot to mount an amp is inside the rear side panels.
If you are running from an iPod you only have a 2-channel stereo output. You do not need a 4+ channel amp. Buy a 2 channel amp. If you want to add a subwoofer, get a 3-channel or 4-3-2 channel amp (switchable) or get a powered sub and a 2 channel amp.
When I did my competition stuff, I used Alpine and Sony amps. They were excellent and I won several awards.
Boston Acoustics has amps now too, and I trust them.
Remember, size does not matter so much with amps. Quality of components does. I used to have a $150 Sony amp which fit in my hand that was more than adequate for daily driving, and better than cheaper amps which were cheaper and "higher" in power. Crack open some of that cheap systems and you will realize you are paying for $10 in parts. Dual and other store brands are guilty of this. You are basically throwing your money away and giving them $75 of profit on an $80 amp. Spend the $100 and get something Sony, Alpine, or Boston. Especially since the truck is so noisy to begin with, you want something that will provide clear sound. This will prevent distortion which will fatigue your ears and give you headaches, and make it hard to listen to the radio for extended periods of time.
As far as speakers, I would recommend the following, in order of performance:
6" round front and rear (best quality)
6" round in front, 6x9 in rear (good quality, more bass)
5" round front and rear (okay quality, will lack bass)
3.5" round in dash and 4x10's in the rear (stock locations, no bass)
The trick is to OVER POWER your speakers. Distortion is caused by UNDER powering your speakers. Not enough power lets the speaker magnet go too far forward and back in the housing, hitting the end, which blows it up. While way too much power can blow a speaker, it's rare. I've only blown speakers using deck power only, never when amp'd. Therefore, get as much power in an amp as you can.
BTW, more power does not mean more volume, it means more clarity. If you want more volume, add more speakers. Each speaker adds about 3db to the system. A 10db increase doubles the volume. Larger speakers also add to volume. A 6" speaker has significantly more surface area than a 5" or 3.5" speaker, which means more volume.
A good set of 6" speakers installed in a proper enclosure (door, panel) which is sealed as best as possible, combined with a good high power amp can sound like you have 10" subwoofers in your car.
As far as speakers, you should go to a local store, put in your favorite song, and LISTEN to all the speakers. ALL of them, including the cheap ones. Listen to them with an amp that is similar to what you plan on buying.
There used to be a pair of Infinity speakers that were $80 which were simply unbelievable. I sold them to everyone when I worked at a car stereo shop, just by letting them listen to them. Not one set ever was returned, either. That was 15 years ago, though, so who knows what it good now. Go to all the car stereo shops you can find and listen to as many as you can.
Or buy Boston Acoustics.
If I were you, I would get the q-logic kick panel 6" speaker pods, and then mount another pair of 6" speakers in the rear side panels just about where the passengers knees are.
http://www.crutchfield.com/p_044C101110/Q-Forms-Kick-Panel-Enclosures-Red.html?search=q+logic
If you want component speakers (separate woofer & tweeter), get a set of 6" for the front ONLY.
If you want a simple subwoofer, Infinity makes a 10" powered one here:
http://www.crutchfield.com/s_108BASSLIN/Infinity-Basslink.html?tp=114
It's nice clean sound, and won't make you deaf. If you install it using carriage bolts through the body it makes it hard to be stolen (ask me how I know ... although it cost me a broken window, the sub remained!) but can be removed easily enough if needed. I put it where the spare tire was.
There are other options, and it all depends on your budget, but there you go.
Finally, as far as the antenna, 31" is the ideal length because that is the size of the FM radio wave. If you get a longer or shorter antenna, you will get WORSE reception!
