I gather you're refering to the motherboard SCSI controller?
There's lots of things to look at, of course you need to check drive jumper settings and SCSI termination is OK.
Use SCSI Inquire (Aminet) to report what the controller is actually seeing.
For some drives, you need to edit the motherboard SCSI prefs (stored in the battery backed memory of the RTC). There are progs on Aminet to edit this. I've found that sometimes you need to enable synchronous, fast synchronous and SCSI2 queing mode to make some fussy drives work OK. Weird, but it can make a difference. Older Seagate Barracuda drives are sometimes bad for that.
If the RTC battery is dead, you'll loose the SCSI settings every time the computer is powered off, so make sure it's healthy.
Check for 5V on pin 25 of the ext SCSI connector.
This comes from diode D800 (near the back of the motherboard) which supplies the 5V termination power to the SCSI devices. This was fitted in backwards in some A3000s, meaning no termination power, which some devices require. The diode can also go open circuit, but can easily be replaced with any common power diode like a 1N4004.
Remove the PhonePak board for now, these caused funny problems on some systems. Add it in later once things are working better, and check the compatibility notes on Amiga-Hardware.com
As for the Cyberstorm's SCSI controller. It uses DMA modes, so the INT_2 interrupt signal is required. This is missing from the CPU board socket on most (all?) A3000D boards. It's easily fixed with a simple wire link modification. I wrote an article on fixing it, available from Aminet or here:
http://amiga.serveftp.net/downloads.html