Occasionally check the airbox for accumulated water. I can't at the moment, but tonight when I get home, I'll take a picture of the "drain" plug, so you can make sure it has no standing water in it...
Other than the chain and airbox, maintenance for riding in the rain is no different. Maintenance in general is all about knowing your motorcycle. Knowing if something is wrong, and then getting it the help it needs. Just think of it as a person. If it starts to cough and sputter, you need to take it to a doc, or learn and be a doc yourself (lucky for motorcycles, any person can do that). To keep your bike fit, trim, healthy and looking great, just spend massive time with it! Lots of sex, um, I mean riding, is a must. Lot's of foreplay, um, I mean cleaning, waxing. Lot's of breakfasts in bed, flowers at work, and a random box of chocolates under a couch pillow, um, I mean, oil change, clean air filter, clean fork tubes and all that jazz..
Luckily, a motorcycle comes with an instruction manual on how to keep it happy, unlike so many women
, and this is a good starting point. However, just like in any good relationship, you have to watch closely, listen well, and pay attention to her/his body language, intonations, etc (communications), to really know what's going on. If you just stick to the manual and it's "schedule", you both will be left reasonably healthy and happy, but getting bored of one another, and wanting to move on fairly quickly.
<Kindergarten cop voice>
So, how much do you really love your ninja?
</Kindergarten cop voice>