Modifying a 512-260B
Great info. Happen to have any pictures of the part change or the duct tape?
I don't have a closeup picture of the changed part (although see below) and it would be a little hard to get one at the moment, but it's an obvious power IC labeled U 15, located behind the VRM heatsink on the left (the orientation I use is that the "back" of the motherboard is the edge with the external connections (USB, VGA, Ethernet, etc.)).
On an older motherboard (ought to check others I have here of that vintage) there was an APL1084 and the newest one I've looked at has an APL1085. Keep the latter part below 64 C and it'll be entirely happy (above that its performance starts falling off although it can run hotter). In the above arrangement the former higher rated part was running at a consistent 48 C when the CPU was running at 40 C; the room was kept hot for this testing, 78 F or higher.
As for the enclosure modifications, I have a set of pictures which are mostly of the work in progress, and that work was split between myself and the friend I built the system for. It's pretty simple, though, especially if you aren't adding a hot Add On Card (AOC as Supermicro sometimes calls them).
First some orientation pictures I took before going wild with the duct tape; this is with an LSI SAS controller and without the mandatory shroud attached:
IMPORTANT NOTE: the orientation of the Dynatron K2 CPU cooler above is suboptimal; initially I just didn't pay much attention to where it was venting. To get it to significantly contribute to the cooling of an AOC, rotate it 180 degrees from what you see here and it'll exhaust in a good direction, plus help keep the Southbridge cool.
With the shroud attached and tacked in place with Scotch(TM) tape:
Some time later after I'd added my mods and my friend had replaced the LSI SAS controller with an Adaptec and had done his own modifications of the duct to cool the AOC:
Anyway, the concept has 2-3 parts. First, construct an air dam so that the power supply's intake is isolated from the rest of the enclosure. That way there won't be a tug of war between its small exhaust fan and the central blower, who's intake area is going to be severely constrained:
Now, to keep your disks cool, use duct tape to require all the central blower's intake air to flow past them. The picture below shows an optimal balance between that objective and getting lots of air into the enclosure to cool a hot AOC, where a single piece of duct tape in the front is covering all the front slots from the air dam to the left, leaving open the last 11. You can cover more, but that will restrict air getting into the central blower, which might matter depending on what you've put in the box and where it lives:
Finally, here's the last AOC duct modification my friend made (made from folded index card paper), it'll give you an idea of the sorts of things you can do. This one splits the airflow coming out of the Dynatron CPU cooler (note that it's been rotated 180 degrees) so that most goes to the AOC but some goes to the Southbridge. Also note the small IC in the lower right corner, I believe that's the U 15 APL1084/5 voltage regulator discussed above: