The A4000D has a really cramped interior. The back of the CDROM unit gets pressed up against the powersupply cutting the PS airflow and pinching the cables from the back of the unit. When considering a CDROM drive, try to find the smallest (front to back) size possible or the drive unit will protrude slightly out the front. The Amiga IDE handle only two drives on it's header.
My A4000 is configured (like most A4000 desktops) with the main system drive and a CDROM on the IDE header. The Toaster/WORK drive and external ZIPdisk are on the WarpEngine SCSI header.
Have fun with your [strike]moneypit[/strike] er, Video Toaster. Oh yeah. check that battery!