For a good ship...
I upgraded in this order:
1) Power Distributor - As said above, this recharges your ship systems faster. They have good ones that are the same or less weight, with better capability.
2) Fuel Scoop - Actually at 300cr, this could be your first mod. Careful refueling though. Choose COOL suns or you will cook.
3) FTL Drive - This will increase your jump range and allow you to add more weight to your ship for weapons, armor, cargo, etc.
4) Thrusters - With a heavier ship you may need thrusters with an optimal weight to closer match yours. A heavy ship doesn't turn well at a decent speed.
5) Reactor - At this point, I needed more power for all of my systems in my Sidewinder. In my current Viper, I actually got a reactor right after the power distributor.
Depending on your play style, you may want to invest in armor and/or shields, although I'd recommend doing that only with a Viper or Cobra (for dog fighting and defense). The Sidewinder is so weak, you'll want to run and jump away before getting into a fight even with stronger armor and shields. Also, the Sidewinder is EXTREMELY sensitive to weight gain. 5.0 tons of armor will cut your jump range down significantly.
With all that being said.....never fire upon me. I will kill you.
Have a nice day Commander.