Get another hosting provided. Just kidding!
If you host is unwilling to drop the fulltext indexing size (which I can fully understand, as you don't want "as","is","a" etc indexed) then you are going to have to deal with it client side.
I think you will find that most bulletin boards (forums) etc that utilise fulltext searching ONLY let you input words greater than three letters when you search. Thus i recommend that you follow suit.
However, if you're adament that you wish to utilise 2 letter words you might like to try a combination of LIKE and MATCH, which will involve you crafting an SQL statement based on the input in the text field provided.
My question to you is this : why/when do you need to search on a "to" letter word
