Chris,
I am not sure of your situation. It is a upgrade of an existing system to AOS ver 5.1 and has become slow after the upgrade to v 5.1? Or have you been running AOS 5.1 for awhile and it has become slower and slower?
As for filesystems, drives, and speed: my experience is JFS is much faster in chkdsk than HPFS. SSDs are MUCH faster than spinning drives on chkdsk and any kind of directory access - like opening a folder - even if both the spinning drive and SSD have the same sustained transfer rate. Spinning drives also have the obvious problem of fragmentation over time.
If you have upgraded AOS and are accessing network drives, and the slow down occurred after the upgrade, could the NIC driver have changed? I have had speed issues using the multimac driver for the network adapter built into my motherboard, which I solved by installing a Intel pro 1000 NIC and using the Intel driver. Don't know if it was multimac, my particular network adapter/motherboard combo or something else in my system. But opening a file dialog box (FOC) was painful because of the slow access to networked drives.
My recommendation: boot drive/partition on an SSD, swap file and firefox profile and TEMP directory on a spinning drive because of SSD wear and potential slow down. Or if you have enough RAM, use a RAM disk for the TEMP directory. If you are using the AOS RAM disk, format the RAM drive HPFS (unless that has been fixed.)
Use/add an SSD even if you are running SATA 2 or slower bus on your motherboard.
