I'm sorry I didn't get to this post until now (though it IS great reading). I don't know how much you have acquired of MacSpeak but I do figure quite a bit by now. Well here are a couple of pointers ... I would give you links but hell if I could remember where I found em :)
1. Now that you are installed and running fine boot with the OSX Installer CD and notice at the top left next to the Apple a menu....click on it and choose disk utilities. Once launched notice on the right a series of tabs. Choose the First Aid tab. On the left choose the drive (partition) with OSX on it. You will notice it now enables a couple of buttons (verify and repair disk permissions) Apple like to own the show here. Choose repair. It gives you output so you can see what goes on. When you are done back out of everything. Watch how much faster the boot is :) Do it from time to time to keep it in good shape.
2. The Apple command key (the one that looks like a four leaf clover), Hold that down on bootup. That is Apple's version of multi boot it will show all OS's it can find to boot (Tip... put your CD in before this process and you can point to an OS on the CD.) A side note regarding the version of "Classic". At work I had a later version of the 9.2.x running fine and when I put it on X it puked.........reason being.... with each version of Apples OS they upgrade hard drive drivers. Apple store proprietary drivers in hidden partitions similar to other manufacturers (Compaq, IBM.....)Even though the version (OS9) you have could be newer (as in my case) the low level drivers wouldn't let it run. The version of "Classic" fit for OSX is 9.2 (though I am getting strange 9.1.3 indentifications with tools I am using). Another thing worth noting is ..... when formating the PHYSICAL drive ... you need to tell it to install the OS9 drivers or you will not get it (OS9) to run period.
3. When in OSX go to system preferences.... you will see a control panel for "Classic" (which I am sure it is poinnting to the correct system folder now)....on the second tab are some advanced options.....choose rebuild the desktop...make this a routine also :)
I could list more but am running out of steam. I hope these things give you back some control of your box .........