I like to fold and I just installed a gtx275 in an ubuntu normally smp folding box. I also followed this guide to set up the necessary "windows on unix" wine environment.
Things that were different for my install ...
1) The mobo I have has built in Nvidea graphics chips (non-foldable Gforce 7100) which caused the Nvidea graphics drivers to be installed at Ubuntu installation/upgrade time.
2) Also because of 1, I needed to make some adjustments in the bios to put the pci-xpress card as the first graphics head and the onboard as second. This is so I can try out the new card and only have to plug in one monitor.
I would suggest that you test the graphics cards and adjusted system for cooling/stability using fancy screen savers, some games etc. Also using the temp sensors.
The step "wine notepad" does two things. Firstly it does indeed create some directories for the wine environment. Secondly it shows that your wine environment works correctly by starting the building accessory application notepad.
I also saw the permissions message on ~/.wine/drive_c/windows/system32/cudart.dll
easilly fixed with a
chmod +x ~/.wine/drive_c/windows/system32/cudart.dll
Looking forward to doubling my ppd with the gpu client, just hope it doesnt melt the PSU &| mobo.
I won't know it it actually works until someone plugs in the Stanford folding server room back in again (power outage today). Currently waiting for both SMP and GPU units now.