I believe are having this problem because you did not install the Mac OS9 drivers when formatting the drive. I do not know of any way to update the drive with OS9 drivers short of erasing it and starting over but I don't claim total knowledge. If you just want to run classic and not boot in to OS9, you should be able to just copy a system over from another computer via firewire or even from a CD-RW.
Will you computer boot from the 9 CD but not let you install, or will it not boot?
The QT problem is a non-issue. you can update it once you get 9 running (booting) or ignore it in classic.