Multiple Problems - Hardware or Software?

Question

I've been having a lot of problems lately with my MacBook Pro and I have absolutely no idea why. I called one Apple store and was told I should reinstall Leopard, do an Erase and Install, and not restore from my Time Machine backup because my file structure or my folder structure or something like that is probably corrupted. Apparently if I restore from the Time Machine backup it will corrupt everything all over again.
That makes no sense whatsoever to me. So I asked my 3D modeling teacher at school (who used to be a tech at an Apple store) and he told me my logic board might be going out, which sounds a little more believable to me. In any case, I'll be taking it to an Apple store on Wednesday to have it checked in and see if they can tell me what's going on, but I figured I'd get some opinions in the meantime. Here's what's going on:
1 - Finder gives me the message "This operation cannot continue because _____ is still in use" whenever I try to delete a file that was previously being used. For instance, I install something, eject the virtual drive, then delete the DMG. I go to empty the trash and it refuses to empty because the file is still in use. I go to Terminal and type "killall Finder" and I'm able to empty the trash.
2 - My PRAM keeps resetting itself for no reason. I'll start my MacBook up and find that all of my keyboard shortcuts are gone, my screen saver has changed, my trackpad settings have been reset, etc.
3 - I'm getting incredibly high CPU usage at random times from random processes. My CPU also spikes whenever exporting a Flash project file as an SWF, exporting a GarageBand song as an MP3, or converting audio or video files (WAV to MP3, MPG to AVI, etc.). CandyBar for some reason takes up about 50-90% CPU on average, repairing permissions in Disk Utility will take 80-95% CPU, and a few other apps I can't think of at the moment have occasionally been giving me problems. Running nothing but Finder can sometimes take up to 30-40% CPU, but it usually stays around the 0-10% range.
I'm finding it hard to believe that this is all software-related, but I don't have that much experience with Macs so I can't really say. Any ideas/thoughts/suggestions? I've already run the Apple hardware test and the TechTool hardware test and neither one found a problem, but from what I've heard neither of those is all that reliable.

Answer 1

Allan - I actually don't have DiskWarrior but I managed to borrow it from a friend who does so I'll post the results after I run it. CandyBar has never given me any problems before, it's just one of the random apps that seem to spike for no reason. I might try uninstalling it if nothing else helps, though.
etresoft - I recently installed ClamXav, but all of these problems started before I downloaded it. I actually haven't even gotten around to using it yet. The PRAM resetting doesn't happen after every restart, and I can't figure out what (if anything) is triggering it, but the next time it happens I'll see what shows up in Console.
As for my CPU spikes, I've been using both GarageBand and Flash for over a year and a half and have never had this kind of problem until a few weeks ago. I've been teaching myself game development in Flash for the past year or so, so I'm constantly testing my project files to make sure everything works and work out any bugs. I'm used to having a slight slowdown while exporting, but this is something else entirely; my entire system slows down (Finder, Camino, everything), my CPU usage goes through the roof, and I get the Pinwheel of Death for a good 20 or 30 seconds before it finishes. Exporting files in GarageBand gives me pretty much the same result except that it takes even longer to finish.
Here's what I found after poking around a little in Console. I'm a complete noob when it comes to the inner workings of OS X, so I'm just posting anything that sounds like it might be bad:
6/14/08 3:16:59 AM kernel vmnet: Failed to clone mbuf: 12.
6/14/08 3:16:59 AM kernel vmnet: bridge-en1: SendToVNet mbuf_dup failed: 12.
6/14/08 4:02:35 PM SecurityAgent ((1778)) (ipc/send) invalid destination port : CGSReleaseShmem : Cannot release shared memory
6/14/08 10:07:05 PM /System/Library/CoreServices/backupd ((2581)) Unable to rebuild path cache for source item. Partial source path:
I replaced the brackets with double sets of parentheses because the numbers were being turned into links.