I've lost track of what computer you have where, and I don't understand why you keep installing buggy OS X 10.4.0 on systems that worked fine under OS X 10.3.9, without being able to update to install system updates afterwards.
That said, you may want to look at this web site for general Mac OS X troubleshooting tips:
http://www.thexlab.com/faqs/faqs.html
In particular, since I know of other people with the same problem as you that fixed it deleting caches, you may want lo look these two pages:
Resolving Disk, Permission, and Cache Corruption
Side effects of System cache cleaning
In addition to some utilities mentioned there for cache cleaning, you may also consider OnyX, if for no other reason, because it's free:
http://www.titanium.free.fr/
Although utilities such as OnyX allow you to clean many caches with just a click of the mouse, I'd recommend to be as selective as possible and clean them up one at a time, to try to identify which exactly is causing your problems, if any. This information, in turn, could be useful for other users. I'm pretty sure some Mail problems are related to cache issues, but I don't yet know which cache exactly is the culprit here (since it was not the Mail cache, I would say that the fonts cache should be next in the list).