I tried to start the car but everything was dead

Check the fuses.

If not you will need a sophisticated scan tool to program the keys.

check ignition switch sir

have a load test done on the battery as there is a dead cell evident.

Change the battery. Newer batteries sometimes go all at once, and are so dead even a jump start won't work. It has happened to me twice. Once you put in the new battery check the alt output with a volt meter should read about 14.5 volts at the battery. If it does problem solved just reset the clock, radio etc.

this doesn't sound good at all. if you couldn't jump start it within a few minutes, you should have stopped right there. maybe you were jumpping the car wrong, from doing so, you may have fried the computer, that rounds your entire engine. try installing a new battery, if any codes were stored in the computer, clear them out. some times just removing the battery cables for a few minutes will do this . sometimes not. try to start the engine. donot jump start, see if will start on its own. if not, seek professional help, keep blaming goodyear until you get results !!!!!!

check for a bad connection like a bad ground at the battery, make sure both terminals are tight at the battery, the starter and the ground at the engine. the shop that installed the EGR should have erased the codes, after 50 to 100 miles you would be able to go through emissions.

check timeing,plugs and spark gaps,distributer points and contacts

this sound to me like at first I thought it was a fuse, as the problem went on it shifted more toward a weak cell in the battery, if a weak cell sits for a little while the battery will not hold the charge in that cell and that will cause loss of power, "its charge", in tne other cells. you had mentioned you used another battery and it ran great but when the battery was removed, things went wrong. You may check to see if there is water in your battery

If you mean key will not turn in ignition,charge or jump start
Car has electronic ignition switch
If battery is low/flat it will not turn

try fittung a larger capacity battery this will help when you are parked for extended periods of time, but it does sound as if you have something draining the battery, try getting the alternater checked