2009 Mac Pro running with fans at full speed after CPU tray upgrade
You must use the original tray from the 4,1.  Cannot put 4,1 tray in 5,1 or vice versa.   If you do, you cannot control the fans.

The firmware upgrade changes the Model from 4,1 to 5,1 but does not change the SMC System Version or the SMC Processor Tray version.  These must match. These should both be 1.39f5 with an original 4,1 or 1.39f11 with an
original 5,1.