Pauses of up to 3-5 minutes are not uncommon. It's a major annoyance. I keep aliases of my hard disk partitions there, and removing them instantly corrected the problem. God knows why it works, but Quake is so much happier. I had to replace the original short 1 drive IDE cable with a standard one of course.
Care has to be taken in dressing the cable as well since it's at the hinge of the side cover.
I've taken photos of the process for an article I'll be posting soon. I've added this info to the updated Yosemite Compatibility page. Michiro Isobe sent a link to a image file of the die showing this feature. Alex Koyshman sent an article on Ethernet called The Network is the Computer . I didn't know he was a 'RC5 junky'.