For a 90 your best hop-up for performance for your money would likely be just a bigger motor if your looking for any serious power upgrade. To push noticably more power out of the 90 you'd have to put about as much money into exhaust, carb/jet kit, intake, etc... as you would just buying a larger motor. You'd have to shop around and see what the numbers work out to, but checking google for "honda clone parts" shows plenty of sites that carry parts for 50-180cc horizontal honda-style motors and parts.
As far as electric start goes if your motor doesn't already have a crank case designed to take a starter you'd need to rebuild the motor with a case that can take one. In that case you'd also be needing to replace the stator coil with one made to run a regulator and battery/lighting system if your stock one's made to just run the spark. What's best for your quad is dependent on your budget, how much performance boost you're wanting, and what your motor already has on it.