Hooking up different sized subs, can't hurt anything. Something else went wrong.
Why do you have 4awg coming off the cap? Is that 3 separate runs to each amp?
Stock batt; it should unless you're in some little import, with a little starter, and a little battery.
Stock alt,
2000w of amp output / amp efficiency (which is usually about 80%), means your amp draws 2500w.
2500w / voltage (14.4) = 173 amps. So if you have the gains set to those numbers, at full volume you are drawing 173 amps. Most stock budget vehicle alts more than 10 years old are closer to 100 amps. Heavy duty pickups and new vehicles might be 150. You need to add almost 150 amps to your stock alt to cover that. A little over 100 more might work.
That's on top of what your vehicle uses. Electric fans, AC, lights, horn, turns, cig lighter, EFI, ... with all draw you will be close to what that factory alt uses. It also depends on the type of music, but you should be looking for about a 250 amp alt. (You're also going to want to do the big 3).