Got my Metra GMOS-LAN-03 in today and tuned up the subs. Not 2 minutes after tuning the door and rear speakers just stopped working. All connectors are fine, and the subs and amp play perfectly. Any help on this?

 

The LT's don't have the Pioneer system, correct?
So if thats the case then the front end is running off the HU ( I didn't see any RCA's on hat GMOS LAN -03)
Is the Alpine HU brand new or is it used.
Its not likely that its a loose wire cuz all 4 speaker getting a loose wire at once, well the odds are out there.
Sounds like you have a problem with the internal amp on the HU but I would have to have detailed layout of the system,

 

sounds kinda like either the speakers are blown or the speaker outputs on the radio fried.. are you getting a burnt smell from the head unit? i had a pioneer h/u that the speaker out puts fried on.. it was an aftermarket h/u though..

 

It has the basic 4-speaker system. And the Alpine is a brand new unit (just installed today!). I'm beginning to think the internal amp is the problem as well and just have a defective unit...

There is no burnt smell at all. Everything else is running perfectly, and before they turned off, the speakers sounded awesome. I don't understand it at all. They just turned off in mid-song and never came back.

 

try takin one of the speakers out and hookin it up to something else to see if its blown and try hookin another speaker up in its place to see if you get any sound out of it that way.. you'll find out that way if its the speakers or the h/u.. if its the h/u then take it back since its new.. they should replace it under warranty..