I am planning to build the MK1 controller board. I am not sure if software is free to use? Also can I use my PicKit3 to bootload the Pic 4550?
Yes, the software is free. You can download it from the official website or using the direct link provided below. There is also a BETA version if you want to try things out.
I didn't see anything about the usage of PicKit3. You can check the Features page to obtain additional information: http://planet-cnc.com/index.php?page=features