God's Peace to you and consolation on your father's passing. Sorry to hear of the family squabbles; hopefully they will calm down.
It's a great keepsake to have a sy�stem that one's family member used. It can be terribly nostalgic, and you should not feel chained to the pieces of gear. The�y cannot love you as your father did. You can sell them, replace them, and mix and match. Truly, they won't cry if you part with them. :) People sometimes hold on to stock shares as well out of nothing more than emotions. Do what's the best for you; your father would be proud of it, most likely.
While erik is correct regarding consistency of hookup of polarity, you will likely want to stay with convention, where white = positive (+) and black equals negative (-). That way at a glance you know what's happening.
To answer your questions, yes, the "Shunyata" would be the Hydra, same piece. He's using both parts of the name in different places of his notes. The reference to "8" or "4" in note number five, regarding the speakers, indicates whether you wish to hook up the speaker leads at the amplifier to the 8 Ohm outputs or the 4 Ohm outputs. These will normally be clearly indicated by their numerals and perhaps the symbol for Ohms or word "Ohm" next to them. You can use either, as he indicated. Typically the 8 Ohm connections to the amp from the speakers may get you a bit lighter sound with more brightness and lighter bass, while the 4 Ohm connections to the amp from the speakers will get you a more solid, weighty, heavier bass sound. You will likely prefer one over the other.
Always triple check connections and turn off gear prior to changing connections. The advice to start with a simple setup is good, but he left you nice, detailed instructions so that completion of the entire system is possible. There is no reason you cannot add in the other pieces and achieve what would be expected to be the best performance.
He left you some beautiful gear, and I think you will be enthralled. If you have more questions, feel free to contact me via message and we can talk on the phone.