It sounds like you need a multi-pass search. Change your indexing options so that 2 letter words and stopwords are not indexed. Then you can do a really fast search for all documents containing the most significant search words, ignoring whether or not they are in a phrase. This is the "qualifiying" round. Next, do a LIKE '%phrase%' search on the rows that matched the first query. This should be a fairly small set, so it will be fast.

If you really have to search for phrases like "in it" quickly, you may have to look into different kinds of indexes and probably read some search engine theory. The Algorithms in Perl book from O'Reilly might be a good starting place.