Unless you are running the version of 10.4 that is on your installation DVD, you should not repair disk permissions while booted from the DVD. The default permissions change with the OS updates, so if you run 10.4.11 and repair permissions using 10.4.3 (for example) your permissions will definitely be incorrect. Use the Disk Utility application from your applications folder for repairing permissions, and use Disk Utility booted from the DVD to repair the disk.
I have updated three G3s running Tiger with the update and had no problems. It did not take as long as the last security update, and generated less hard drive noise than its predecessor. (Thankfully.) Did you get things to work on your G4? Have you run Applejack? Personally, I never bother with archive-and-install. If I am reinstalling, I: download/burn all the needed Apple updates to CD (I don't trust Software Update); backup; test the backup; boot to Tiger DVD; open Disk Utility; zero out the disk; boot OS 9 CD; reinstall OS 9; update to OS 9.2.2; boot Tiger DVD; install Tiger; apply combo update, security update, Quicktime, java, etc.; install latest versions of apps compatible w/Tiger; drag over any wanted data from my backup. I repair permissions in Tiger after installation, combo update, security update, iTunes update and Safari update. Erase/install is faster than archive/install, but it takes a while. I feel this method saves disk space and lessens the chance that any corrupted data will be carried over with the reinstallation. Just my opinion, and this methods works well for me. YMMV.
(Version 2009-005)