Update: Got my EKA code this morning, car accepted the code....still didn't work, no remote function, alarm still triggered by the key in the ignition, and engine immobilized. So I was just getting ready to start taking the headliner out to get to the receiver (I don't have a sunroof so can't do the easy access method) and I had to push the car out of the way for something. Put the key into the ignition to unlock the steering and noticed the alarm wasn't firing so I fully turned the key and the engine fired up.
So yeah....baffled. Engine starts fine now, however the remote still doesn't work so I'm still going to have to remove the headliner to check the receiver and at the same time check the Alpine window seals as I'm sure they're leaking.
Thanks for the replies.
Further Update:
Just decided to disconnect my battery, leave it off for a while, and reconnect it before taking the whole headliner down.....yeah that fixed it my remote works now. I feel stupid. XD Still have to take it down at some point to check my Alpine windows but still, a bit of a relief.