BootROM reconstruction is a very different process than a cross-flash with the MacEFIROM tool, where you just upgrade the EFI part of the BootROM and everything else inside the image is kept MacPro4,1. An early-2009 Mac Pro cross flashed by the Netkas forum method, what we call an MP4,1>5,1 hybrid, have just the MP5,1 EFI and all other components of the BootROM firmware image (the NVRAM/BootBlock/hardwareIDs) are still MP4,1 versions, this cause several problems like the impossibility of using Firmware Restore CDs and makes an MP4,1>5,1 hybrid much more susceptible to bricking.
SMC: The 1.39f5 SMC firmware version is independent of the BootROM and immutable, it's not possible to use a mid-2010/mid-2012 CPU tray with an early-2009 Mac Pro backplane, or vice-versa. When the SMC firmware version is mismatched, the SMC micro controllers will enter fail-safe mode and will run all the Mac Pro fans at the fastest RPM, all the time. It's like being on the side of a jet turbine.
Nehalem vs Westmere Xeons: Apple supported dual CPU Nehalem Xeons officially up to El Capitan. While up to High Sierra, the dual CPU Mac Pros that still have Nehalem Xeons work perfectly, Mojave don't support dual CPU Mac Pros that still have the original Nehalem processors anymore. A dual CPU Mac Pro that still have the Nehalem Xeons will KP when waking from sleep and the audio will have maddening stuttering problems when running Mojave and newer macOS releases, the only way to solve this is upgrading the Nehalem processors to Westmere. Only MP5,1 firmwares support Westmere Xeons, MP4,1 firmwares don't support it, the firmware reconstruction, or the cross flash to MP5,1, is a requirement to run Westmere Xeons. Single CPU Mac Pros don't have the waking from sleep and the audio stuttering problems, just the dual CPU ones that still have Nehalem Xeons.
BootROM Reconstruction: Reconstruction is a service, you dump the SPI flash memory with ROMTool or flashrom, take pictures of the ESN and the MLB labels, send me and I'll reconstruct a new BootROM image tailored specifically for your Mac Pro, based on the generic 144.0.0.0.0 upgrade image, with the MP5,1 firmware standard (MP5,1 EFI/NVRAM/BootBlock/hardwareIDs).
After the reconstruction, your Mac Pro will be identified as a MacPro5,1 and be able to run Mojave officially/natively if you have a METAL supported GPU. While an early-2009 Mac Pro flashed with a reconstructed BootROM image will have the same BootROM firmware specification of a mid-2010 Mac Pro, the serial number is kept the same and when AboutThisMac validate the serial remotely with Apple it will display that you have an early-2009 Mac Pro, this is cosmetic only, software support will be the same as a real mid-2010/mid-2012 Mac Pro.
I've sent you a PM with detailed instructions, if you are interested.