The CD-ROM in the Quadra is indeed SCSI, so that doesn't indicate whether or not your IDE bus is bad.

Almost every brand of hard drive you'll find should be jumpered to master, except for Western Digitals, which should have no jumpers at all.

What version of the Mac OS are you booting the Quadra with? I would certainly try another hard drive on the IDE bus along with zapping the PRAM at least 4 times.