I wound up starting completely over. I re-installed Arduino, continued having bad luck with Jarduino, but I was able to get another aquarium controller sketch called Stilo to work. Except after loading the first screen it just flashes and reloads every second. I think this is because I don't have the RTC installed yet. I will do that today.
flc, thats a good idea to check out dorkbot. They have a meeting tonight, I just might have to stop by.
I never tried Stilo myself, but it sounds odd that not having an RTC installed would cause the entire sketch to reset itself every second.
Usually, without an RTC, any time/date functions won't work. The only thing I can think of is that the sketch relies on the RTC to do something (i.e. check on the status of the sketch so that it can request new data from the temperature/pH probe), but there are better ways than querying the RTC.