I have both of the above. I plan on upgrading both. The 5,1 will be more work than the 4,1, but not by much. If I keep the 4,1, will I eventually wish I had ket the 5,1 (2009 and 2010 respectively
Besides the normal GPU/CPU/Memory/HDD diferences that you expect, the things that really distinguish an early-2009 from a mid-2010/mid-2012 Mac Pro are:
early 2009 Mac Pros:
Backplanes and CPU trays have SMC version 1.39f5.
Dual CPU tray use de-lidded Xeons, single CPU tray use lidded ones.
Early-2009 dual CPU tray heatsinks can only be used with an early-2009 dual CPU tray.
You can only use CPU trays made for early-2009 model (SMC 1.39f5).
Models that have Wi-Fi from factory, have AirPort Extreme model BCM94321MC, that only works up to Sierra.
mid-2010/mid-2012 Mac Pros:
Backplanes and CPU trays have SMC version 1.39f11.
All models use lidded Xeons.
Dual CPU trays heatsinks can only be used with a mid-2010/mid-2012 dual CPU tray.
You can only use CPU trays from mid-2010/mid-2012 models (SMC 1.39f11).
AirPort Extreme BCM94322MC that only works up to Mojave.