Yes, getting lint on the back of the glass panel is a big concern. Apple supplies a sticky roller to its service personnel to remove any stray lint or dust. Your best bet is to work in a very clean area and lay the glass panel on a soft lint free cloth as soon as you pop it out and then immediately cover it with another lint free cloth and don't mess with it till your done.
Also, try to find a service manual for the aluminum iMac online. These will not be on the Apple website as they are not for public distribution but if you look hard enough I bet you could find one. Any model of Aluminum iMac will do, the disassembly is all the same.
That being said, if you have applecare, LET APPLE SWAP THE DRIVE! Its not that hard but there is a chance you'll screw something up while your in there.