Is there any reason to run a ground wire from the main breaker box to the water line(right next to where it comes into the house) if the water supply line is plastic that enter the house?

With lightning rods on the house would I need two grounds on the breaker box?

Can I use the lightning rod that's in the ground to ground the electric box.

If your box is currently grounded to plastic pipe, it serves no purpose and is ungrounded. Have you ever tried a circuit tester? What does it say?

Lightning rods are not grounding electrodes, although they serve similar purposes.

You do not need to bond water lines near the entrance. Just anywhere accessible.

Your electrical service should have at least one grounding electrode of some sort.

Without knowing the reason for your questions there is not much more to add.

I am changing out all the galvanized pipe and going to PEX, the line from the well is plastic and that what is just inside the exterior wall. I have tested outlets for ground and they are.
Thanks for the advise.

Kophie,
As stanfortyman mentioned you do need to have properly installed grounding electrode(s) connected to your electrical service. You say that you do read a ground at your outlets... the may be only the neutral conductor connected to the transformer that supplies your service. For safety purposes and as required by the electriacal code you need grounding electrode(s) also.
A grounding electrode makes a connection to "earth". The earth has it's own polarity which varies over time and conditions such as moisture and salt content. The connection to the electrode will tend to bring the earth to the same polarity (near zero volts) as the grounded conductor in your electrical service. This is something you want as anyone who has ever touched a ground wire in a not so well grounded basement can tell you. It also does give a lightning strike a good path to the earth and not just your house.

This is worth your effort!
Be Safe