Ok so i have read conflicting reports about whether or not we can step up to a higher output alternator. Some say due to pcm control we can not? im looking to run about 1300w rms stereo system using not very efficent JL Slash series amps, so im thinking the stock electrical system is going to be crying for momma. I know the first thing to do is a big 3 upgrade, but then ive read that putting a big power wire from the alternator output to our batteries positive terminal is a no no as well? just need to clear up can a big 3 be safely done on the liberty, mine is a CRD by the way. Also will a higher output alternator work as designed with the pcm control? if so whats the options out there for alternators?

I don't see the need for the alternator yet. I ran close to that much power in a lil ford escort with a 55w alternator, and no issues. The alternator is there to charge the battery, not run the electrical system. It'll overheat in short order if it did. Your battery is the principle source of power. Having the grounds hooked up correctly and wired correctly(this is the biggest issue that even the audio shops fail at) will insure you won't have lights dimming etc. Maybe reinforcing it with a 1farad capacitor, but that's it. Remember, electricity is made of matter, and you can not create matter from nothing. That said, what you take from the battery(positive side) must be returned to the battery(negative or ground side). If you have a 4ga cable coming off to power the amp, then you need a 4ga cable going from the battery negative terminal to the body ground. Otherwise you have everything electrical in the vehicle, including the amp, trying to squeeze power into a lonely 10ga ground strap.

mine is a CRD, so not sure it makes any differences as far as engine grounding needs. I plan to run 0ga for a battery postive to alternator post, and battery negative to like the shock tower bolt perhaps id think that would be a good ground point, now how about the engine ground does it need to run back to the battery negative from say the alternator bracket, with 0ga as well? lastly i leave all the factory wiring alone and simply add the new correct? Also do i need to fuse any of these links im adding? and if so at what rating?

You're likely going to ground the amp to the body near where you have it mounted, right? In which case you will want to add the second ground to the battery from the battery to the body somewhere. Shock tower would be a good spot, as you want it kept as short as reasonably possible. Leave the rest of the electrical harness alone other than what is needed to hook things to the battery. As far as fuse rating, you absolutely need to have the power feed fused near the battery. Otherwise if something cuts the wire, etc, and no fuse to blow, it'll burn your vehicle to the ground. As a general rule, the fuse should be about double what the load will be. If you have a 40amp load, you want an 80amp fuse, etc. You'll need to find out how much power the thing draws, and fuse it accordingly.

i understand i need to fuse the amp lead. im talking about the line from the alternator to the battery, i see some fused, some not.

I wouldn't worry about the stock harness at all. It won't affect what you're doing. Just need to fuse the power to the amp.