I bent up the RF shield inside a bit to clear the scan doubler, and then mounted the harddrive to the shield with double sided tape (not very strong stuff, made for carpet). Everything is very secure. The drive now sits circuit board up, but that's no problem. And, since I left the RF shielding the FCC won't come knocking on my door. ;-)
Mounting the VGA connector was a little more complicated in my case. I had previously used the expansion port next to the joystick ports, but I wanted to use my Blizzard SCSI at the same time. So, I desoldered the RF modulator from the motherboard, carved the hole open a bit more to fit the connector, and hot glued the VGA connector circuit board to the motherboard where the RF modulator was. The result looks very good, and I no longer have wires hanging out of my machine.