ATI Tray tools is for the graphics card if the fan is too noisy and you can have custom 2D and 3D clocks too. I underclock my HD4830 in 2D mode and it runs cooler.
IIRC you cannot downclock the GDDR5 memory on the HD4890 currently but pushing down the core clocks to the lowest possible does help.
You can get the middle fan out as it seems other people have done this. You may need to disassemble part of you case though to get to it though.
If you are looking at an SSD this 64gb one could be used as a boot drive for the OS only and is not badly priced at £115:
http://www.hexus.net/content/item.php?item=19889&page=1
Crucial and Novatech do Quidco cashback too!