First and foremost, welcome to saltwaterfish.com! You have a very nice looking tank. Congratulations on finally getting one up and running. One of the first things I would recommend is to get more live rock. It will save you in the long run.
1) Is it really worth it to get a refractometer, and how much money are we talking about?
Yes, it is definitely worth it. I would not set-up a saltwater tank without one. They cost about $50.
2) I'm really debating about the lights. I would like the MH that clips on the back of the tank (150w, I believe). I haven't actually seen the MH at work so don't know what the look really is. I prefer whiter-looking light, but understand there is some need for blueish light? Please fill me in. I like the idea of moonlights, as well, the little blue LED ones. I don't know where/if I can find a fixture with both in one, that doesn't look like franken-tank.
Also, keeping it cool? do the built-in fans work well enough if it's not right on top of the water?
It will work just as well with the glass top on the tank, right?
Personally, you do not need metal halides. How long is the light on the top of your tank now? I may be able to recommend a very good light set-up that will not break your bank account. I just need to know what you can fit up there.
About the glass tops, personally, I do not see a problem with them. I use glass tops on my tank and have no problem doing so.
3)How many fishes can I really have? I don't mean inches. I don't get the inches thing. I'm reading about the different fishes and all, but with trying to decide and keeping all the information straight, I'm getting quite confused. I'm having a hard time with conceptualizing the scope of fishes I can get. How many smallish (clown and smaller) with at least one medium one (as in coral beauty)
Your stocklist for the most part sounds fine. The only things that I have a problem with are the mandarin and the anemones. The mandarin needs a bigger tank (or less congested tank so that pods can reproduce quick enough) and anemones absolutely need metal halide lighting. Also, the blue linkia will not work either, since these guys need at least a 125 to prevent them from starving to death.
There are no fish that help with cycling. Adding anything now would just unneccessarily kill the animal.
4)Also, same question with corals. Does it just depend on how much sand surface and live-rock surface i have to place the stuff?
You could have tons of corals. You just need to make sure you have room to place them all and give them enough space so that they are not touching each other.
5)What about inverts? the more the merrier the cleaning crew, as long as they get along together?
Yep, you do not want to be ridiculously overstocked, but you could have a ton of snails and hermits as long as you have enough live rock to support them.
6) What kinda chemicals should I stock with the rock and the fish?
A good test kit is the first thing you need. You need to test for pH, ammonia, nitrite, nitrate, kH/alkalinity, and calcium. Other than that, I would also recommend getting vitamins for the fish. I just recently started using SeaChem's Reef Plus and Garlic Guard and I like them a lot. I also like Zoe, Selcon, and VitaChem. Also, Marc Weiss' Coral Vital is a very good supplement that has a lot of trace elements in it. The only other things you will need is what your test kits tell you that you need. For example, you may need a kH buffer or calcium additive.
7) When topping off, I can just add un-salted RO water to the wet-dry? What do I need to check besides temperature when doing this? (how do I fix whatever I'm checking if it doesn't match?)
When you are topping off the tank, all you need to do is add unsalted fresh RO water and make sure the temp is the same as your tank. That's it.
