Ok so I got 2 jl audio 12-w3's on a sony class d amp. System sounds and works great once it gets going.

I am having one problem, the system fails to initialize amplification.

Basically, the amp turns on whenever my radio turns on but i either have to play my music very loud or heavy bass. Another option is to unplug and replug my audio input on the amp and it works. I am having trouble figuring this one out. Once it initializes, i have no problems, i can lower the signal and it hits fine unless i turn the radio off and on again.

I got ground to the body, 12v from the battery, rem is to radio accy.

My audio input is speaker level inputs wired to my rear passenger pillar speaker.

 

Try a line converter rather than speaker-level inputs -- or better yet get an aftermarket HU if you've been thinking about it.