Recurrent problem in Mac OS 9

[chemistry_geek]

After a really bad crash last fall, my computer exhibited strange behavior. The problem was that for every mouse click, a WHOLE SECOND would pass before the action was carried out. I couldn't figure out what the problem was and still haven't. I thought the problem was solved when I archived everything on my HD to CD, zeroed the HD, then reinstalled everything from the ground up. Everything was fine until another crash, now the lag returned, but not as bad. I don't think it's an extension conflict/problem because the system only started acting funny after the crash. I have the standard Mac OS 9.1 install that came with the Mac OS X CD. Extra drivers / extensions include: Logitech Wheelmouse, Hewlett Packard DeskJet 970Cxi printer and 5300C series scanner, Adaptec Toast 3.5.7 CD burning software, Microsoft Office 2001, iTunes, AOL instant messenger. Does anyone know what this problem is and how to correct it?

chemistry_geek

[Clarifix]

I don't like the Logitech mouse software. I bought another mouse (a Macally, later an optical Intellimouse) just to get rid of the software.
The mousewheel software is not extension software, but an invisible background application, that quits and does not work anymore after e.g. using an installer application that quits all running apps, but doesn't require you to restart. I remember using Peekaboo just to get the Logitech software running again without having to restart the Mac.
What I mean is, that given the fact that you have to wait so long after every mouse click, it could be your mouse software having corrupted it's preference file, or worse.

The first thing to do, is to check if you have this mouse problem after you started up with the shift key - no extensions loaded.
If that works well, trash your mouseware (was'nt it called mouseware?) preference file. Better still, trash all the mouseware files and reinstall the mouseware application.
If it doesn't work (starting up without extensions), it means that your core system software and/or prefs files are damaged. Bad news: reinstall from scratch is the fastest way to resolve your problem. You COULD try to locate the problem file (I once found out in the way explained below that my file sharing extension was getting corrupted), by starting up from the absolute minimal configuration: System, Finder, ROM file, system resources file, maybe carbonlib, but certainly Text Encoding Converter - maybe i am forgetting somes files here. Make sure you can still startup from CD.
After starting up from the absolute minimum, you can gradually work your way back to the complete system software, each time testing for the problem, and restarting with a few files more. Time consuming, but in the end you will find the responsible file(s), making a fix of the problem easier later on. Your choice.