Mac Pro/Illustrator/In-Design - not responding???

I inherited my Mac Pro from a past colleague at my office. I have tons of design work I need to do but I'm finding major problems with the Mac.
For instance - I will open an Illustrator or In-Design File - this could be something I have saved on the computer or it could be something I have just downloaded - either way - when I open the file and go to "Save As" or "Save" it takes the Mac 2-3 minutes (if not longer) to save the file.
If during this time I look at the Activity Monitor to see what is occurring - the program says "not responding" but when I'm in the program and try to move the mouse - the color wheel is processing indicating something is happening.
This happens every time I try and save any file type. I think something in the computer is corrupt and I'm not sure what to do for a resolution.
My helpdesk cannot determine the problem. What should take only a few minutes to perform is taking 30-45 due to how slow the computer is. The same problem occurs with pdf files too.
I've ran the software update and also repaired disk permissions but still no luck. We wiped the computer of the old users info and created a new account under my name - I'm not sure if this would have caused the problem.
Please help on this - it's getting extremely frustrating because everyone I've talked to says this should not be occurring with this computer but no one knows how to fix it.
Buy a new set of drives. One for system, one for scratch, one for media files, one for backup. That is a good start. Then add enough drives for backups so you have backups of system; of data; two sets or more; and emergency boot drive.
Make sure you have more than enough memory. Graphics? 8GB is a good start. If you work with 2GB files, double that.
Don't rely on Apple Disk Utility First Aid, Alsoft Disk Warrior at the least - and you need to repair the drive and files, not just running Repair Permissions. Maybe a good How-To on maintenance and troubleshooting manual.
Start from scratch. If you are using Leopard, buy 10.5.6 DVD and use that to start with.
If you use SuperDuper to backup and clone your drives; and Disk Warrior to repair the drive and file system you will be a long way - but at this point, keep the old system and files where they are as "backup" and copy everything to new drive to work from.
And if you work with large files, then working off stripped RAID for scratch and saves helps. Do not use the same drive for the system AND scratch editing AND for files and media libraries. Separate those out.
Some tips that focus on Photoshop but also at configuring a system.
http://macperformanceguide.com/OptimizingPhotoshop-Intro.html
http://www.adobe.com/go/kb401089
http://www.macgurus.com/guides/storageaccelguide.php
http://www.macgurus.com/guides/photoshopguide.php

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https://discussions.apple.com/thread/5772339?tstart=0
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