I recently got a 15" stereo integrity mag and an ma audio hk1397, Im currently running 4 awg wire, but my question is should I just replace the power and ground with 0 awg or replace the rca's and remote wire as well? Also I will be running the sub at 1000rms and my amp is only 90 amps will I run into any problems ( I will be doing the big 3 in 1/0 gauge soon)

 

It's touhg to get much info on this amp. If the power terminals will accomodate 1/0 wire, by all means replace it; power wire is a GREAT investment (assuming you will have the big 3 done ASAP).
Don't bother with the remote turn-on wire. As long as the amp is turning on, thats all that needs; just to sense when to turn on- it doesn't draw much current there. If you have multiple devices (amps, x-overs, fans etc) being turned on my your head unit, add a relay on your amp turn-on wire to make sure you don't burn that out. You have what you have with the alt; do the big 3, upgrade the wire if the amp will accomodate, and see what happens...gently. If you experience sever light dimming or voltage drop look into a seconf battery in the trunk. the only other remedy beyond that is a pricey HO alt.