Your app looked quite promising until I loaded an epub to work on.
It took quite a while to load initially (which is ok if other things are fast) and once loaded I tried to search for a single word. not very fast but ok. I noticed there was a blue progress bar under the search entry field which seemed to be moving.
I then typed in a two word search term (consecutive words) where I knew the words were near the end of my epub. It took over 2 minutes for MarginNote to complete the search.
I opened the same epub in iBooks and did the same search. It was completed in less than a second.
This is simply too slow. A research tool must be able to search much faster than this. After waiting for the epub to load I thought at least some text indexing was taking place, but no.
It doesn’t really matter how fancy once can organise notes etc if you can’t do searches in a timely manner.