A clean install is the best way to go.
That said, if you uninstall all the drivers that you can before you swap out the boards you will have a better rate of success.
If your Raptors are in a raid configuration currently, that my pose some difficulties for a swap
Also the age of the current OS install will also pose challenges, the older it is the more trouble that will pop up post swap.
I once did a swap of an nVidia chipset board for a newer one that seemed to work ok at first. But over time it started to become unstable and a full drive wipe and install was needed to fix it.
But I install and remove software on a constant basis. I run reg cleaners and all types of OS maintenance software but even that will not stop the gradual decline of an MS OS over time.
I would go with a clean install personally.