+1 on this. I'm thinking Ignition Switch or wiring leading to it.

 

So now... everytime I do anything like having the ODB reader on or checking the battery, the car doesnt start. I have to put touch the negative and positive, then lock/unlock the doors. Maybe its a remote alarm issue?

 

The obd reader port is on the dash/column loom. How do you check the battery?

Have you any issues with the rear lights? because the security locking module controls them, there might have been an issue with the flashing additions you fitted, a burnt out component on the circuit board within the slm.

Have these quirks been a recent thing? like after you fitted the flashers?

 

when I went to Autozone, i had them check the battery voltage... as soon as he finished, the car wouldnt start.

The blinkers are off now, the only other thing i noticed is the transmission delaying on WOT recently.

I am nearly going to take it to the dealer, this is becoming too complex of an issue.

I have new bushings and shocks going in the front end, which by the way, i disconnected the CATS module...

 

Don't be concerned about the unplugged module, it's non cats' now, at least that's how the car's system sees it.
Lighting additions are now off the car, and the connections are super soldered and shrink wrapped? (by this I mean the twist and tape method will not do)

Check the column wiring.
To remove the steering wheel, lower and extend for max space, you need to unbolt the airbag from the back 2 x torx, drop the battery, a highly remote chance of earthing the wires and it goes off...
once the bag's out of the way, you'll see cruise and vol wiring, disconnect them and unbolt the wheel by the centre boss. Wheel lifts off. Now you can inspect the stalks wiring. The upper and lower cowl removed exposes the ignition wires. This is where I would start. It's an 03' (02' to me)for christ's sake!
You know what happens when that car goes to the dealers....I've seen 2 big bills....