If the Heatsink- pipes are solid (which they should be), you should be able to file them down by a few mm's. Just so long as the vanes still have room to 'crimp' on to the rods.
I know it's stating the obvious, but move the heatsink waaay away from the PC internals when doing so
Another way to grab a mm or 2 would be to remove the mobo and file/grind a mm off each end of the (usually) 6 brass stand-off's (if fitted). You'd need to check for clearances underneath the mobo, though - Too much off the stand-off's will short the mobo to the mounting tray and it will all end in tears
