Here is an update from a day's debugging, sigh
I reinstalled Phocus and now it is working (do this after the 2.3 RAW update).
I tried reinstalling Aperture and the RAW 2.3 update and it is still not working with the following problems:
1. with Aperture Quick View off then when a 3FR image (from any camera and back) is selected the image will show a preview during the "Loading" message and then turn white. If you try and perform any adjustment on the image the Aperture thumbnail will also turn white and then the image is essentially lost - i hope it is not eating the original.
2. images often have a magenta cast on the left or top and a cyan cast on the right or bottom (depending if it is a horizontal or vertical format shot). The color changes right at the CCD's stitch boundary so this is probably an equalization error in Apple's RAW converter (or DCRAW which I "think" is the open source code Aperture's RAW converter is based on).
3. some images show with violent color shifts and posterization, sometimes black with magenta and sometimes wild color shifts, looks a lot like cross-developing C41 in E6 process
4. no matter what camera RAW image i am working with I will sometimes get the "unsupported image format" purple screen of death and then every image will be unsupported until i quit Aperture and restart it.
I have sent files and system profile to Apple. If anyone else is having issues let me know, more data will help.
Thank you,
Glenn