Ok, so it seems my best bet is to try and clean the drives, right? Is there any easy way to do this? I already tried to take them apart, but having the plastic case off don't make it easier to reach inside.

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Some options for you:

http://www.welovemacs.com/acc-6000.html

http://apple2.info/wiki/index.php?title=Floppy_Drives#3.5_in._Drives

You may well need to dismantle the drive further to get at the heads and give them a cleaning with a Q-tip and rubbing alcohol, if you elect not to get an automatic cleaner. It's a delicate job, so be careful if you undertake it.

You might go the bare-metal bootstrapping route (http://adtpro.sourceforge.net/bootstrap.html) and see if you can get a catalog of any of your disks once you get ProDOS running via the serial port.

Getting a SCSI drive to a bootable ProDOS state will be a tricky business indeed. If you have a SCSI mac that could do the partitioning and formatting (plus copying over the ProDOS system files) it might just work. You'd need an earlier version of Mac OS than OSX, though.