I have had no problems (ah well, not scsi/disk related) on both my A4000D or A3000D. In all cases I only used SCSI because it performs really well. I used many different controllers including the Cyberstorm PPC, mk2, WarpEngine 4040 and the onboard A3000 SCSI controller, both old and new chip version.
I suspect there might be something b0rked in your install, maybe the best way forward is first to remove additional hardware in your system and reinstall. Just go with CPU accelerator + RAM + SCSI + DENEB + Video card. That should be a working combo...
What I did was to go from a clean 3.1 (just floppies with Picasso96 and IDEfix) to 3.9, then added BB1 and 2. I can copy for hours without issues, on both machines. Not tried BB3 and 4 yet, and the 3000 gives a recoverable alert at bootup, probably from an FFS related update somewhere but works fine otherwise.
For backups I use network and USB. As USB flashdrives are quite cheap I use a set of them, but I could also use an external USB drive. I wrote a 5-line crappy bug-ridden instable script that just LHA's my complete system drive to an archive file on the USB stick and optionally network drive (FTP).
edit:
As a system drive I just got two Seagate Savvio 2.5" 10K SCA drives from Ebay for about $25 each. They hardly make any sound and are quite fast I think, probably faster than the SCSI bus can handle anyway. Haven't had time to test or try them yet beside putting power on them to test. I wanted to go the SATA - SCSI way but $150 for an adapter is a little too much for me.
