First of all, like choosing a monster, you just more or less choose the level of the disease (generally within +/- 4 of the players average level or some such). If your disease is inflicted by a monster (something like mummy rot) it should be the same level as the monster.
Second, the DCs for the progression of the disease (page 42) have been errata'd. When in doubt use the hard DCs of the appropiate level for your disease as your recovery check, and then a medium check as a no change and anything below that as worstening. (and you can check this out on page 19 of the errata document if you feel so inclined, about half of the diseases had a stray +1 but otherwise followed the page 42 dc's perfectly).
As an aside but probably helpful comment, the attack value should be disease level +2-3 if against fort and +1-2 if againts a different nad
Third, is highly subjective and depends on how much you want the players to hate the disease. Most effects are A-Okay to use with the exception of anything that robs standard actions and movement (Dazed rather than Domination/Stun, Slowed rather than Immobilized). These effects are still okay to use but makes fighting around the disease very hard. Stealing healing surges is also A_Okay, but generally keep it to 1 or 2 unless its the shadow death from the shadow shadow bo dadow. Then fuck those players and take half a dozen healing surges.
I think there should really be no particular reward to the disease. Diseases generally show up either as a feature of a monster or a skill challenge thingy. If you wanted to count a disease as a Complexity 1 Skill Challenge of the diseases level it probably wouldn't be too far off the mark.
(requiring a roughly 4 skill checks to cure or something like it, if it spreads the complexity increases, complexity 2 would be 2-3 people , complexity 3+ is more like a trad skill challenge in that they are probably solving the problem rather than treating patients.)
Here's an example from something I saw way back in a blog.
Flail Chest----------------Level 9
Your enemy's blow crushes your rib
cage, leaving you with a rattling,
dripping wound that won't heal
Attack: +12 vs Fortitude, Improve DC
21, Maintain DC 16, Worsen less than
16. First check is 1 min after
inflicted, further checks every hour.
The Target is cured <---> Initial
Effect: the target loses a healing
surge and is slowed
Secondary Effect (gangrene): When the
target is Bloodied, the target gains
Vulnerable all 5
Final Effect (sucks to be you):
Whenever the target is hit while
bloodied they are knocked prone
Hope that helps :D