Please can you attach the output of the following commands:
hdparm -I /dev/sda
hdparm -tT /dev/sda

Additionally, there is an interesting message in your log file :
[   12.511114] ata1.00: ATAPI: HL-DT-STDVD-ROM GDR8164B, 0B10, max UDMA/44
[   12.511114] ata1.00: limited to UDMA/33 due to 40-wire cable
[   12.526835] ata1.00: configured for UDMA/33

but this should not slow down your hd because it's connected on a
different channel. It doesn't hurt to unplug the dvd drive and see if
it's still slow.

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Disk I/O is very slow, system freezes for seconds
https://bugs.launchpad.net/bugs/268588
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