- Does this mean I get the special qualities of the said swarm or does this mean i only get the no weapon dmg?
The bit you quoted just means that your HP doesn’t change and fire and area-effect spells and abilities can damage you. Out of context, it doesn’t say anything more than it says.
The actually-important bit is
In all other respects, the swarm shape ability is identical to the druid’s wild shape ability (see Chapter 3 of the Player’s Handbook).
Here we can look up wild shape, see how it works, and know how swarm shape works. Really, this line arguably should have come first, but whatever.
Going to look up wild shape, though, we have something of a problem: errata changed how wild shape works after Savage Species was published. When they wrote that swarm shape behaves like wild shape, wild shape behaved like the polymorph spell. Later, they errata’d wild shape to behave like the alternate form special ability. So you will need to ask your DM whether or not the wild shape errata also applies to swarm shape. I would argue that it should, but the rules are vague on the subject.
For completeness’s sake, here are the relevant rules from both:
So you definitely do not get the swarm subtype and definitely do not get the swarm traits (which are listed as a special quality).
This is rather awkward, since without the swarm traits, the line about taking damage from fire and area-effect spells is meaningless; of course you do, nothing suggests you wouldn’t. Ultimately, master of flies is very poorly written and you’ll probably have to talk to your DM about it. Personally, though, I’d be leery of even using such a poorly-written class.
- Does this imply something with the special qualities as well since it dosen't just say centipede swarm?
Why would it? The only thing that means is that you turn into that kind of swarm.
- How does the size translate to swarmsize, does it mean I'm occupying 9 squares if I'm medium from the start?
If you are Medium, two size categories up is Huge, which has a Space of a 5×5 square. Swarms are amorphous, though, so presumably it just means you’re talking about 25 contiguous squares.
- Lastly, is the damage from swarms boosted by natural attacks? I ask since natural weapons are weapons that are physically a part of a creature and it's stated that they attack their target and they don't really have anything but natural weapons.
No, it’s not a natural attack—it’s not an attack of any kind at all. It’s just automatic damage. Ultimately, the rules are kind of unclear about it, so again, probably something to discuss with the DM. By the rules, though, I’m pretty sure the only bonuses that would apply to that damage would be bonuses to “damage” with no caveats or qualifications of any kind. Attack damage, weapon damage, natural weapon damage, and so on, swarm damage is none of these things.