I don't think it's wise to replace the CPU trays SMC, there are several hardware differences between 2009 and 2010/2012 dual CPU trays, from the heatsinks to components on the PCB.If you want to use genuine 5,1 tray with 4,1 (flashed to 5,1) logic board (as per the OP's situation)
You can either
1) Solder a 4,1 SMC chip on to the 5,1 tray. Therefore, you can have a dual processor tray that can use normal lidded CPU, with 4,1 SMC on it.
2) Solder a 5,1 SMC chip on to the 4,1 logic board. Therefore, you now practically make your cMP identical as genuine 5,1. Able to use 2010-2012 tray (but cannot use 2009 tray anymore).
If you gonna replace a SMC micro-controller to match CPU trays and backplanes, replace the backplane SMC. Backplanes are totally identical between 2009 and 2010/2012, besides the SMC firmware version.