[...]
> 
> These scratch partitions should be preserved if possible...
> 

Then just tell setup-storage to do that: 

disk_config disk1 disklabel:msdos bootable:1 fstabkey:uuid preserve_always:3
primary  /        10000    ext3  rw,noatime,errors=remount-ro
logical  swap      2000    swap  rw
primary  /scratch  0-      ext3  rw

will keep the /scratch partitions at precisely where it was before. No need to
care about cylinder locations or whatever.

> I'll use parted -s instead of setup-storage...
> 

As you prefer...

Anyway, hope this helps,
Michael

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