KJ won't start, security light stays on.

[joooooooooop]

My 06 Liberty wont crank and I'm thinking there's a problem with the security module or its communication.
It sat for about 3 weeks since I last drove it. Tired to start it but it wouldn't crank. I took out the battery and recharged it for like 24 hours (at 12.5v now) and also connected the +- cables on the car to try and reset it. Tried jumping the starter relay and the starter works. Tested the pins to the starter relay, 85 never get grounded by the ECM. Tried park, neutral, gear doesnt seem to be the issue. The ignition switch also sends 12v to the starter relay so its not that.
The red security light on the dash never turns off. It blinks once for like half a second after you put the key in and it just stays solid after that. Then after about 5 seconds the airbag light comes on. Taction control light is always on too. The security light also does not blink when the car is off and locked, and the alarm does not go off if I lock the car and open a door from the inside.

Does anyone have recommendations for a diagnostic tool and software that can read security system codes?

Other things to note:
Connected another car battery (13.3v) in parallel with the battery.
The battery is only about 4 months old, but got down to 11.9v after sitting for 3 weeks.
Tried both original keys.
Tried locking, unlocking the driver door trick.
Checked all relevant fuses.
Brake pedal feels very stiff, usually its soft even when the car isn't started.
When turning the key to the start position, the radio turns off as usual and +12v is sent to the starter relay.
All other electronics, lights, windows, power locks, AC, work as usual.

 

[joooooooooop]

I also tried taking the chip from the spare key out and pitting it as close to the SKIM module as possible in case its a signal issue but that didnt help.
I also unplugged the SKIM module to see what happens. The security light doesn't come on until the key is in the Start position, also the airbag light doesnt turn on.

 

[LibertyTC]

Load test that battery, a fully charged battery should read 12.6 volts.
Have you tried doing a hard re-set?
Tape & isolate the positive and negative cables together for 45 minutes & see if that helps.

 

[joooooooooop]

I did take out the battery to charge overnight and I held the two cables together but only for like a minute.
I also tried connecting another running car's battery with jumper cables which also didn't help.
I guess I can try taping the connectors tonight and charging some more.