Hi,
You'll have to reformat those partitions to change cluster size. If you choose NTFS as the file system when you install W2K, it will atuomatically set 4,096 bytes as the allocation unit size if the partition being formatted is larger than 2 gigabytes in size. Beware of converting partitions. When you convert from FAT or FAT32 you wind up with 512 byte clusters. I suppose that may be how you would up with the cluster size you have on those partitions. Partition Magic, AFAIK, is only able to convert cluster sizes on FAT / FAT32 partitions.
You can reduce some of the deleterious effects of 512 byte clusters on performance by keeping the MFT, pagefile and registry hives (as well as a bunch of other files) defragged. The defragger W2K comes with doesn't do this, but many aftermarket defraggers do. I suggest using one which defrags the registry hives, pagefile and MFT at boot time. That's the method Microsoft recommends. (Norton Speed Disk does it on the fly. Seems like a great idea, but I don't do stuff to the OS that the writers says not to do.) I use O&O on some systems, Diskeeper (the bigger brother of the inbuilt defragger) on others.
Regards,
Jim