Alarm going bats#$t crazy

[Dead Reckoning]

Hey guys, 06 SR5, just pulled the battery cables to clean, when I reconnected them the alarm goes crazy. I hit the unlock button on the fob, jumped in turned the key to "on" and manually tried locking/unlocking the truck with the key. No good, alarm still going off.
Pulled the horn fuse to shut everything up, but I can still hear the hazard lights clicking.

ALSO there is a small aftermarket looking red led that is mounted on the dash that is flashing, which I'm assuming is an aftermarket alarm system?

Any suggestions? The rear hatch's electric closer motor is dead (getting it replaced tomorrow) so the rear gate is bungee-ed shut, could this have anything to do with the alarm not shutting off?

Thanks!!

 

[BlackWorksInc]

Yup... Aftermarket alarm system...

If you remove the kick panel under the dash you should be able to see where its connected into. Most of these alarms are just tapped into wires, so you can just pull the harness out of the factory wiring like pulling a parasite out; typically you will need to cut and reconnect the ignition wire as that is actually connected in series with the alarm. All in all an easy repair to do.

 

[Dead Reckoning]

Yup... Aftermarket alarm system...

If you remove the kick panel under the dash you should be able to see where its connected into. Most of these alarms are just tapped into wires, so you can just pull the harness out of the factory wiring like pulling a parasite out; typically you will need to cut and reconnect the ignition wire as that is actually connected in series with the alarm. All in all an easy repair to do.

Gotcha, thanks. I pulled the panel and I see a two added wires (about 16 gauge) around the fuse block that have in-line fuse holders. Pulling the fuses didn't stop the alarm, but I'm sure they're connected because except for a stereo there are no other aftermarket electronics in the truck.

 

[Dead Reckoning]

Whew! Finally got the alarm shut off, found the brain box after trying the valet switch (which was broken) and went ahead and removed the alarm system by disconnecting the wire leading to the box.
My question- I only disconnected the wires to and from the box, I didn't trace them back and and take out the splices in the factory harness. Do I need to? The alarm is off and the truck cranks and drives so I'm assuming I'm ok?
Will eventually have a shop remove everything but am I ok for the short term?

Thanks guys!!