I believe most of the complaints I am getting about lost or broken functionality are based on a series of AJAX issues with 4.0.1 which are all slated to be fixed in the next patch that should be released on the 4th of February. I'm holding out for that patch before I do any major code digging since its so close.
I'm also going without the paypal donation system because it hasn't been updated to be compatible with 4 yet. If you feel an overwhelming urge to donate though you can donate to the paypal account which is firstname.lastname@example.org
I'll of course keep you posted.
Most of the graphics issues for the upgrade have all been worked through, and I'm currently quite pleased with the way the site looks. I hope you all are too. There's still more work to be done of course, but its coming along. Thank you all again for your continued encouragement and participation and most of all patience.