So, basically, you want a short primer for most of the field of motion control? You'll probably need to read a number of textbooks to get that :-)
1. Find the kinds of sensors you want to use, and read the data sheets for those sensors. It could be anything from two-phase quadrature relative encoders, to full digital encoders with SPI or I2C interface, or parallel gray code output (popular with optical absolute sensors) or an analog voltage (potentiometer-based encoders.)
2. You need to be specific with what kind of I/O you need, and what parts you have available. "How to develop a SPI interface when I'm using a Xilinx FPGA" is very different from "how to develop a robust analog sensor for a PIC microcontroller."
3. You can probably find any kind of bus. Most common are CAN bus, Ethernet, RS-485, TTL UART, and step/direction. Although "controller" and "communication" are so vague as to be useless. There are controllers that use WiFi for communication, or optic fiber, or mechanical devices.
4. Again, you're going to have to either look for textbooks, or go to an academic search such as citeseer or google scholar or whatever.