Hi James, and thanks for your question...
I really think it is a mistake to treat the notes and rhythm as separate things. Usually when people do that, it is because they are trying to go too fast and work on too many notes at a time.
If you go slowly enough and tackle your pieces one measure at a time, you will be able to play and count out loud correctly from the very beginning. It's only through working that way that you will truly master your pieces. Otherwise, you are making a lot more work for yourself and setting yourself up for a lot of frustration!
Please read my blog post on efficient learning at viewtopic.php?f=4&t=4
The main gist is that you learn each measure slowly, hands separately, then hands together, always counting out loud and playing very carefully. If you go slowly enough, you can play anything!
Let me know if that helps!