Resolved New here, bad electrical problems

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I’m 16 with not to much hands on mechanical experience and I need some help. The other day I was driving and my theft light started blinking, my dash went dim, my radio kept shutting off and it was raining. Then the theft light would blink really fast if i tried to put it in test mode (on the odometer where you can test gauges, battery, see codes, etc) and it wouldn’t start but if I didn’t do that it would start. Fast forward a few hours later the GEM module was clicking really fast (sounding like the blinker was on) and I unplugged it and plugged it back in. It stopped clicking but wouldn’t start. I was also trying to remove the transmission for a 5spd swap in the middle of all of this, forgot to disconnect the battery and with an extension grounded out the starter on the headers. Now there is no power to anything in the car except when no key is in the seat belt light is on, battery light. When i put the key into accessory mode (1 click) the theft light blinks about every one to two seconds and then when I turn it to the on position (2 clicks) only the battery light pops up but the CCRM makes a clicking noise just once. Also with no key in the alternator hums. Tried new PCM and CCRM and still the same no crank or anything. Someone please help!!
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