"Spinning beach balls" mean that the CPU is tied up. Programs using heavy memory CPU, or drive intensive apps, can all cause spinning beach balls without anything being wrong with the system.
Scannerz I believe, was designed to catch two types of errors:
- Drive head crashes/bad sectors.
- Developing problems with the system.
The latter is more interesting and the way Scannerz does it is by using surface scan progress as a reference. If a drive has bad sectors, they'll repeat at the exact same location(s). If errors are showing up from another source with no regard to the surface scan progress, then they being caused elsewhere in the system.
I'm not writing an essay on Scannerz, instead check out these if interested:
http://www.scsc-online.com/Downloads_files/Troubleshooting%20With%20Scannerz.pdf
The two common types of problems with a unit are those that lead to catastrophic failure (blown CPU, I/O controller, supply, etc) which leaves the system dead, and the other types are those, as described by the OP that allow the function to operate, but not correctly.
Regarding the troubleshooting, the unit needs to be opened up and all connections, particularly to the Bluetooth and Airport card need to be checked. One way to do this is to remove them completely, and restart the system to see if the problems persist. If they go away, re-install them one by one and see if it can be associated with one device only. The Bluetooth is located in the right back corner near the display hinges. You would probably only need to disconnect the cable to see if that's causing problems. The Airport card is on the left side, probably about 1.5 inches from the back. It seats into a slot and is secured by screws. These don't pop out like they used to on the Aluminum PowerBooks. Once again, I would just unseat it without removing the antenna cables to test it. I've never seen a Bluetooth board cause problems like you're describing, but I have seen Airport cards do it. On the old Aluminum PowerBooks if the cards slipped out a little (mostly on the 12" models) it could actually lock up the system.
The types of shields that you used to see on the iBook are gone. The top shielding is integrated into the top that holds the keyboard and trackpad. I'm sure this is described on iFixit (or other sites) but you need to carefully lift the top up as if you're tilting it towards the display to release the cable.
What you could do is remove the top of the unit, which leaves everything visible, plug in a USB keyboard and mouse, and fire the unit up with the external drive and test it with both Bluetooth and Airport disconnected. If the problems clear up, it's one of them. Plug each one in and see if the problems re-appear. If they do, you've got your problem isolated.
If the problems are the same with the keyboard/trackpad, Airport, and Bluetooth gone, then you've probably got a crack in a trace on the logic board somewhere. The so-called "irregularity" that Scannerz detects is from the system going into constant read/write cycles as the CPU or I/O controller tries to pass data on data lines with an intermittent connection. When the connection is open (not making contact) read/write operations fail. When it closes, they succeed, thus the timing takes longer than it should have.
If I was to take a guess, I would say either an Airport card problem or a crack in one of the traces between the CPU and the I/O controller. If it's actually the Airport card, that can obviously be replaced. If it's a trace on the logic board, it's likely impossible to fix unless for some reason it's highly visible. I suppose the connections to the Airport card's logic board interface could be problematic as well, but I would think that it's unlikely. Believe it or not, just removing and re-seating the card(s) may correct the problem (if that's it).
I would guess that cracked traces on logic boards are responsible for between 30% to 50% of the logic board failures. I also suspect this is the reason that Apple moved away from plastic units and moved strictly to aluminum casings (pure speculation on my part).
As an FYI, I think you'll find the MacBook a lot easier to work on than an iBook. Much better thought out in terms of serviceability.
Good Luck.