power kills when I hit the brakes, not enough power to light an LED help!!!

[fullmetal]

Car: 91 240sx sr20det swap battery relocated to the trunkok so I drove my car around all day turn off turn on, off, on, etc. i drove to the post office dropped a letter in the box then went to turn my car back on and nothing, no click no fuel pump pressurizing nothing. I looked at all the connections and nothing appeared wrong but every time i hit the brakes the clock reset. so a lady there gives me a jump at the battery which has been moved to the rear about 3 min of charge and nothing. my brother comes up we try again this time in the engine bay and after letting it charge for about 15-20 min it starts right up but if I hit the brakes or turn on the lights the power of the entire car pulses enough to turn the radio on and off. I get home turn the car off then right away try to turn it back on to check if it will and again it does nothing. I pull the battery and take it to pep boys to have them check it, its fine. I reinstall it and figure check the power across the terminals to see if it is the alternator and after trying to jump it with my dads truck and letting it charge for about 20 min the LED's in the dash are finally at full brightness I try to crank it and one thump and all power is gone again. I repeat the jump for another 30 min to try to make sure it works (sucking the tank dry on that V10 Ram) and same result. does any one know what is going on? I was thinking the alternator was messed up and letting the power drain back through the system. But I have no idea if this is right at this point cause the system should still be able to charge if this were the case. can any one point me in the correct direction?