Well as far as bar position goes, that's totally an individual thing, some want more height, others don't, some like OEM. I did a quick eBay search and came up with these two
Gearing is another one of those things, some like a short gear, some tall, being that most of my riding is just cruising around, I went short, I dropped my RPMs at HWY speeds about 1k, I did lose a little bit of acceleration, but hardly noticeable to me anyway, I can still almost pick the front wheel up shifting to 3rd. If your going to play with the gears, I recommend changing the front sprocket, for 2 reasons, 1 they are cheaper than the rear cost wise, 2 it's a lot easier to change than the rear, and get steel sprockets, forget the aluminum ones.
Gauges, totally your call on that one, I just glance down at mine once in awhile, but I did do some carbon fiber wrap so they look better I think.
Customizing preference is up to the individual, that what makes it so cool, hey it's your bike, your money, he'll if you wanted to paint pink dots on it LOL.
Some things like suspension tuning, engine tuning is gonna be lets face it boring, time consuming, and nobody see it, it you will feel the difference.
I recommend start with the easy stuff, it's offensive the cheapest too, and see where it takes you. I'm also added something to mine, so it's a work in progress, with really no ending, and I like it that way. I have a 500 as well that I did the same thing too, had it for 7 years now, and still messing with something on it.
The only thing that holds you back is the money, unfortunately.