Wow, congrats on the huge pond rehab! Here are a few suggestions: aeration is super important, especially if your pond gets a lot of sun. What you might try is getting a secondary pump with a fountain head. That way one circulates the water and the other aerates. Some products I love are Simply Clear, which adds beneficial bacteria and enzymes, and Tetra's Barley and Peat Extract. If you have a problem with jumpers or predators, I suggest getting a nylon net cover.
Www.drsfosterandsmith.com carries them and they're inexpensive. I also suggest getting solar yard lights and putting them around your pond. They're a nice accent and they have a safety function. Home improvement stores sell all kinds for about $3 to $5 each.