Save it as a last ditch effort as removing the ram is quite difficult, especially if you've got full 16MBs.
BTW, do you have the CyberSCSI module attached to MK-II by any chance? Just checking, as some A3000D users with setups like yours leave their cases open so that CyberSCSI could be attached to MK-II. Anyway, if you are using CyberSCSI, then perhaps it is the reason for the native SCSI problems, as the two may be conflicting.
If you only have a bare MK-II card, another thing to try would be to modify the native SCSI controller's settings through SetBat utility (available on Aminet) and see if you get a combination of settings that tolerate your accelerator.
A3000's SCSI controller can be a pain to work with sometimes.
