"Manually building the firmware" seems like a great path ahead and I think us failures should get together and try to work on this. The scripts/programs are great when all the variables are stable & constant but to accomplish things like this it's better to have an annotated procedure where we can adjust to differences and problems during implementation. I'm looking at the underlying scripts for the Tool to try to develop such a manual procedure but struggling a bit.
I'm also looking back to old posts around flashing the Mac Pro 1,1. A lot of the discussion then was more "hands on" and conceptual then, as opposed to now everybody just trying to get the damned Tool to run when obviously in some environment it just can't anymore. I'm hoping I can learn enough about the firmware updating process from these 1,1 flashing posts to get my head around ithe current situation with the 4,1. It's become an obsession far beyond reason. I've done a whole bunch of these in the past mindlessly just running the Tool and it annoys me that something has changed and by just blindly using the Application I never learned what was actually going on and can't readily adapt.
What does your System/Library/CoreServices/Firmware Updates folder look like? Mine looks like this and I think it's wrong (obviously the USB thing is irrelevant but just being complete):
What does your RamDisk look like. Mine looks like this and I think it's wrong, mostly because I get the same RamDisk even when Tool fails.
Most of the people are getting it done just fine and some of us are failing. It's genetic probably.
Conclusion: I gave up and got rid of the 4,1. I don't often do that.