1. I don't think AGM batteries are really worth it. Maybe you're lucky and it lasts twice as long as a flooded acid battery, but it also cost twice as much and did it really give that much benefit over the other?

3. 2 gauge should be fine for you. If you're not running a winch or other high draw devices then it should be very sufficient.

4. We can't really determine this for you, get out a piece of string and run it along everywhere that you think you would attach your wiring. Be aware that the engine does move somewhat side to side and you don't want your wiring to be tight. Whatever you measure out, add extra to that length when you order, even like an extra foot of wire per cable. You can't stretch that stuff, and the extra $2-3 in cable is not worth the hassle of being to short.

5. 500A fuses are to big for your application and your wire size. In the factory dual battery setups for the diesels the batteries are wired in parallel to each other, just straight wires, positive to positive, negative to negative which essentially creates a single 12v battery with double the capacity, no fuses in between. Fuses are debatable for this situation.

The way you want to think about fuses is, any wire that can be energized can burn through and catch things on fire. If you are OK with your wires melting/burning through while going over the top of the firewall or over the radiator support, etc, then don't bother with fusing them. In some instances it won't matter what is below the wire, maybe it's just open air or laying on the frame where it won't really matter if it were to fail in such a catastrophic way. The main way these large gauge wires would get damaged would be in a really terrible car crash, and at that point other factory wires may catch on fire or fuel lines, etc so you can't really mitigate every unknown.

If you do choose to fuse, then you have to select your fuse based on the wire's capacity to carry current. 1/0 wire is good for somewhere around 300-350 Amps sustained load so you would not want to fuse higher than that on that sized wire without taking some risks (wire length factors into this as well, shorter length can allow for higher loads).

I have used this calculator before for a good estimate on sizing wire, Wire Size Calculator

6. Your alternator is fine, very good actually.

 

Whatever you decide to do, take lots of pics and show us how you did it in a How-To Article.

 

I second that as I want to run a second battery. My truck came with the extra battery tray and some other wires from my main battery not going anywhere,lol

 

For comparison, here's what they were installing in 2023.
Keep in mind that about 2007 GM switched to computer monitored/managed/controlled charging system.

The Duramax has dual batteries standard. (and the 2003 duramax would also have had dual batteries)
K48 is the code for adding dual batteries to a gas 2500/3500

 

It was '05 or '06 when they switched to computer-managed charging.
Duramax has dual batteries, hooked in parallel, for starting. IDK how the dual battery option for gas trucks were wired up.

 

In the early NBS (99-06) there was a simple isolator mounted to the firewall that was ignition triggered and connected the 2 batteries together. I saw it posted somewhere before, but I don't think it was a very prevalent option.

 

I hooked mine up parallel when I did it.

 

I sure hope you did. If you hooked it up in series it would let out the magic smoke.

 

On my 2000 Silverado i just used the Duramax battery tray that bolts to the firewall and fender on passenger side.
Ran some 1/0 welding cable from battery to engine block and hot to the primary battery with a decent wire covering to protect from chaffing.