Nah... I moved the same drives over from a 3,1 and didn't have an issue. Plus, I took all the HDD's out and booted with just the SSD and didn't fix. I also disconnected the SSD and tried to boot with only the HDD bays and same result. If it's not the firmware, what the hell else could it be?
It's really hard to tell. You are now comparing a 3,1 to a 5,1. Which is not just a firmware upgrade.
If you want to narrow down to that's a firmware issue. You have to:
1) Remove the W3690, because that only works with the 5,1 firmware.
2) install the original CPU back in.
3) Time the HDD show up time.
4) downgrade the firmware back to 4,1
5) Time the HDD show up time again.
And if the manager really show up much quicker. Then
a) Re-flash it to 5,1
b) time the HDD show up time once more, to make sure it's not because the unintentional reset during shaping CPU / firmware flashing, etc (e.g. SMC reset).
You are now just keep blaming the 5,1 firmware without any proper control test. How can we make that conclusion?
However, from your above test. We can confirm that my 1st assumption is wrong, it's not due to the number of HDDs, but something else.