Lights first as I'm guessing you will need them soon if you continue to commute.
Second a cheap repair is to replace your cables with new stainless steel ones. It will probably improve your shifting and braking and if you are seeing rust, it probably needs done. Replacing the housing at the same time is not much more expensive and is even more effective if things are rusty.
As for an upgrade to your performance, nothing is better than clipless pedal and shoes. However this will probably run you between $100 to $200 depending on your choices.
If you are comfortable with you saddle leave it alone otherwise look at different models there. More expensive does not necessarily mean more comfortable for you but you may have to try several before you find one you really like. (I'm partial to Brooks)
For the rest of the components, use them until they wear out or break then replace with better within your budget.
Craig