I am interested in upgrading the wiring that came with my e-80
chartplotter, S1G autopilot, wind machine, and speed/depth instrument.
What are good reference matierals to read, to plan this out?

Talk with Raymarine. Their website support folks are pretty good at
answering complex questions.

I want to accomplish:
- autopilot recieves wind direction and speed
- autopilot recieves way point information from charplotter
- chartplotter receives data from all instruments

If you use Raymarine gear all this should interchange via Seatalk cabling.
Just a matter of stringing wire from device to device in a daisy-chain sort
of setup. Shouldn't be much trouble at all.