Have a secondary machine handy with which you can image a narrow (50 pin) SCSI drive and issue a low level SCSI format command. To do this, I use a Windows 2000 PC with an Adaptec 2940AU SCSI card installed. The nice thing about this setup is that it's old enough to run GEMExplorer to read TOS filesystems but it can also use the (much faster) Selfimage imaging tool. [TBD: Remove the requirement for the SCSI-enabled PC after "dd" is available on sysinst. Should be in NetBSD 6.]
You will need a PC with a 1.44mb floppy drive to create the Atari install floppies. Have two blank 1.44MB 3.5" floppy disks handy. Format them on the PC to make sure there are no bad sectors. Extract the latest TT Advanced Utilities Disk to a third 1.44MB 3.5" floppy.