Installing a virgin 9.x should work with a 6.3.3 backup. If you uninstall AC, it might not uninstall SQL, so you might also have to delete that as well.
A question is whether your backup files work, as I have seen backup files that do not easily restore. While I have not done a 6.3.3 to 9.x, I suspect that alone should not be an issue. You would have to do a database tune before you could open it. The tuner can take a while to run going from 8 to 9, so it will probably take longer with a 6.3.3
I would recommend doing a dummy trial where you take an unrelated computer, install 9.0, do the restore from the 6.3.3 database and tune. If it works you can take a backup of that and put on the clean install V9 you do on the actual server and just restore the V9 backup from the test. If it doesn't work, you know ahead of time without erasing a working system. Then you could call for help with the restore.
But then, how large is your system and database. Will you really benefit from going to SQL 64 vs 32. On a small system without a lot of users, you might not see that much of a gain. Which means, before you put in all the work to create the 64 clean install, know that you are getting the performance gains making it worthwhile. The easiest route would be just to upgrade in place your current 6.3.3 and leave SQL intact at 32 bit.
