Although I'd gotten up to 1300+ characters and lots and lots of words, I recently nuked everything and started over, and it's been a really productive step. I don't know if other people are as scattered in their studies as I was, but I had bits and pieces of all sorts of different lists, random items I had added to my queue, etc. and nothing really hung together in any sort of systematic way. I was also uncertain if the words I was practicing were words I would actually find useful.
When I started fresh, I chose a few small lists with useful words: parts of the body, clothing, and Chinese provinces and cities. As my main source of characters I started with the "1000 most frequent" list. I used the 500 most frequent characters to find words in the Skritter Word Finder (I forget who built that tool, but it's insanely useful) and added the first couple of thousand of those to my queue to reinforce the characters and learn their contextual meanings. Since the word finder sorts by frequency, I can be certain I added only common words.
One problem I ran into is that the "Delete All" button is extremely slow. I don't know what you guys have in the backend, but with a database it would be very quick to do a "delete all from ... where userid=?". As it was, it looked like it was deleting items one by one from my queue and my set of characters to study, and it took many hours to complete.
Another problem is that the Word Finder doesn't have any limit on the number of words it finds, and when I put 1000 words in as input it locked up. I wouldn't imagine that most people would need to add 10,000 words at a time to their queue, so allowing people to control the number of words returned would probably give much better performance.
So, I don't necessarily recommend that others follow suit, but if you're frustrated with the set of words and characters you're studying it can be very satisfying and motivating to start over in this way.
James