The heat sinks for the dual processor 2009 Mac Pro, per the Service Manual, are part numbers 076-1329 (CPU A) and 076-1330 (CPU B).
For 2010 and 2012 they were part numbers 076-1367 and 076-1368.
As the 2010 and 2012 use CPUs with the Integrated Heat Spreader (IHS), it's logical to conclude that the heat sinks were changed to accommodate the required additional 2mm of clearance for the IHS. Further, as only one part number is listed for heatsink A and for heatsink B for 2009, it is further logical to assume that all the disparate CPU versions used in stock 2009 Mac Pros came without an IHS. Were this not the case, more than one part number would have been specified for the heat sinks for the 2009 Mac Pro.
Further support for this reasoning is shown in the fact that the single heat sink for the 2009 single CPU Mac Pro, part number 076-1338, was the same part number used in 2010 and 2012. And the 2009 single CPU Mac Pro uses an IHS CPU, as do the 2010/2012 versions.
Finally, only one processor board is listed for the 2009 Mac Pro, part number 661-4998. That part has no retaining spring or cover for an IHS CPU. By contrast the 2010/2012 processor board, part number 661-5708, clearly shows the retaining spring and cover for an IHS type CPU.
Bottom line? All stock CPUs used in the 2009 Mac Pro came without an IHS fitted, and like precautions should be used for all models when reinstalling the heat sinks when the stock CPUs have been replaced with CPUs with the IHS fitted.
We knew that. There are many a thread in this place regarding the replacement of the lidless 09 CPU's with their lidded counterparts. What lead to that post?