Well...you'll probably get varying opinions...but here's mine.
Originally posted by Elk Chaser
I am planning on getting a new alternator somewhere around 94 to 120 amps (is that enough?).
Yes. Make sure it is a marine unit, and replace the stock wire with a beefy one to keep from frying it. Also, run the wire away from the engine (as much as possible) to keep it from soaking heat.
Originally posted by Elk Chaser
Installing one new Optima battery to power the engine and necessary blowers etc. (is that enough?)and then using the two existing batteries I have now for the stereo system (is that enough).
I used to run a three battery setup with my last (2,000+ watt) system, and it worked fine. Two batteries for the stereo is a good start, but it's really gonna depend on how much the stereo draws, and how you listen to it (how long with the engine off).
Originally posted by Elk Chaser
I know the proper way is to install an isolator to separate the batteries but do I need to separate the two stereo batteries as well (either requiring two isolators or one three way isolator)
I used to run an isolator, but got better results when I removed it (went to Perko switches). In fact, I still have a 3-bank marine isolator if you want it (I think it was $120 new).
Originally posted by Elk Chaser
..AND does the capacitor need to be isolated as well?
No.