My amp kx1200.1 works only 5 minutes and then getting real hot somebody have any idea

You need to swap your main battery for a high performance kinetic... and maybe even ad a small kinetic in the back as well (fused separately) and see how that works for you. Just one oversized kinetic battery replacing your stock battery may do that trick. Remember, its best to install two batteries of the same brand and size, its ok to use the same brand and two different sizes (a kinetic 2400 and a kinetic 600 for example, but with an isolator) but its easier and simpler to just put in a kinetic 1200 or something that will replace your stock power sucking ineffecient lead acid stuff.

I got a stock head unit (monsoon in a 02 Trans AM) and i put a 200 amp alternator with 4 gauge wire through everything, my amp is sx1250.1 kicker pushing a JL 10w0, it will push my sub just fine when my volum is low. i know it has plenty of power to push it but as soon as i turn the volume up on my head unit it says "low voltage: on my kicker. i also got a 1 farad capacitor too!! do i need to get a new head unit or is it something else???

Http://www.kicker.com/faqs

This is saying you are running your impedance to low on your amp. You need to wire your subs in 2 ohm or 4 ohm configuration.

http://www.crutchfield.com/S-R23Xlj4sko3/learn/learningcenter/car/subwoofers_wiring.html

2. What speaker impedance loads do I need for proper operation of my Kicker KX and SX series single channel (.1) amplifiers?
KX and SX series subwoofer amps will perform perfectly at a speaker impedance load of NO LESS than 2 ohms. KX1200.1 and SX1250.1 amplifiers make maximum power at 1 ohm. Using impedance loads below Kicker recommendations will not make more power but it will eventually damage your amplifier (it will trigger the amps over-current protection) and void your warranty.

Hope this helps!