IBook acting strange...erase and reinstalled...it's starting to be strange

My iBook was acting strangely...I can't connect to the wireless server, though ISP, network settings and Airport are all correct and the connection is visible and the strength of the connection will change. I cannot load any internet pages. In addition, my iDisk icon disappeared, then on restart, it reappeared, but I have no access to it. A "copy of previous iDisk" then appeared on my desktop with all of the contents, but I can't move them from this version as it says I do not have access. So, I started looking at the logs, to see what, if any, errors there were. I didn't have access to the security log and a few others - although I'm the only user account on this computer. Needless to say, I'm no expert so I "spotlighted" some of the things showing up in the logs. Spotlight returned articles on Apache and XTools (Xcode?) - neither of which I installed (I think Apache might come included). I looked and sure enough, XTools was on my hard drive with many, many files - most with the name or extension of pb or pbx. I started to dig a little deeper in the program and noticed some scripts in the vein of when user enters/types "xyz" initiate process or replace with "zyx", etc. I saved some of these files to the desktop, powered off and restarted. When I opened the desktop after the restart, all of the files were in the trash - not by my doing. I removed them and locked them to the desktop until I could figure out what happened. Then, they disappeared, my computer shut down and when I tried to restart, I couldn't get past the spinning gear.
I took this to the store, they checked it, said they could recognize a drive, that I should archive and reinstall. I did this, things still acted strangely. I called AppleCare, they said to back up everything and reinstall.
I did this, now am finding repairs are needed through disk utility for security and authorization priviledges. I repair, go back in a few hours, run it again, just to satisfy my curiosity and the same repairs are needed for disk permissions.
A friend has uttered the horrible "trojan horse" phrase to me...as I download regularly from LimeWire. I'm not sure what a next step would be to free the iBook of it's quirkiness.
Sorry for the long post...but it's been an eventful few days.
iBook G4   Mac OS X (10.4.2)  

You can ignore any permission repair that states "We are using special...". I'm not sure about Tiger but Panther has a few others that come up if the cron maintenance scripts have run.
Other than the repeating permission repairs, is it running OK now?
John

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