For what it's worth:

1) When it comes to rounds is it worth the money to get something like Winchester Ballistic Silvertips or am I just as well of saving some money and using Remington/other rounds?

As has already been mentioned, "premium" ammunition isn't necessary for any of your intended uses. Core Lokts, PowerPoints and the like will perform quite well on deer and black bears.

2) I know "grain" is a weight measurement but what is best practice with what to use? I know some people pick the medium grain so they still get a good speed and knock down power without sacrificing to much of either.

In a .30-06, you'll probably use 150 grain bullets for everything up to and including deer, upping to 180 grain bullets for elk or moose.

3) Are lower grain rounds better at one thing where higher might be better used on other things?

See above

4) I know I should spend between $300-$500 on a good scope, any recommendations as far as brands or even specific models?

I don't think it's necessary to have any more glass than a 3-9x on a .30-06. Most of my workaday rifles wear either Burris Fullfield IIs or Leupold VX-2s and VX-3s. Nikons seem to have a faithful following within this price point, but I don't have any experience with them.

5) Is it best to still stick with a 100yd zero when dialing in the scope or should it be zeroed in higher?

I'm going to break with the pack here. I zero EVERYTHING dead-on at 100 yards. Why? First, my targets are calibrated for 100 yards. Second, I can see the target a whole lot better at 100 yards than I can at 200 yards. Third, I keep ballistic tables out to 500 or based on reticle stadia (Ballistic Plex reticles, etc.).