I have researched level two farming, but cannot find the fish... the window that pops up says that I have enough technology to clean the ocean, just that I need to find the fish. I also have level two engineering.

Any help would be appreciated, thank you.

Try looking at the strategy and puzzle guide. The link is:
http://www.ldwforums.com/ubbthreads/ubbthreads.php?ubb=showflat&Number=53282&page=1#Post53282
and then just click on Lady CFII link

Since the word (Spoiler) is not in the head of this post I will tell you to go look in the guide
Good luck.