Mac OS X Lion freezes, mouse pointer still moves, HDD still busy

Hello, I need some help with a problem on a MacBook Pro (15-inch Core 2 Duo). Mac OS X will lockup. The clock will not advance, any GUI animations will freeze. But the mouse pointer can still move, and will switch between a beach ball and the normal pointer sometimes. I can still attach to this Mac using file-sharing. Also the screen dims after while. However other things like keyboard brightness won't adjust.  This last time I noticed Spotlight was in the middle of a scan, I can still hear the HDD working. The caps lock indicator works, but keyboard commands like ctl+shift+eject (pur display to sleep) don't work.
Remediation:
     The HDD was formatted and Mac OS X 10.7.3 has been reinstalled
     TechTool 5 surface scan of the HDD: passed
     Apple Service Diagnostic: looped for 16hrs, all tests passed
     Apple MRI: passed
     Reset PRAM and SMU
Upgrades/modifications:
     RAM was upgraded to 4GB
     HDD was upgraded to 750GB
     The battery was removed because it had failed some time ago

I've tracked the problem down to bad VRAM, it seems that the windowserver freaked out causing all but the mouse to freeze on the display. It should be noted that in the frozen state I could still take screenshots (Command+Shift+3). The resulting .pngs were solid black.

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