Thanks for the info guys. I was a bit nervous to try a CFW in MFW Builder, but I will give it a try tonight.
I noticed something weird about updating a MFW with the blu-ray patches.
Every time I update I get the blue screen which says my settings are corrupt, and need reset.
When I try to reset them through recovery menu it doesn't work, just keeps sending me to that blue screen.
The solution I found was to wipe the partition table of the disk on a computer.
Once I do that it goes through the initial disk formatting, and everything boots fine.
It's really weird, because for a split second before the blue screen comes up I can see the initial configuration options where you choose a language.
I tried swapping hdds in, and out.. One of the disks I had was in this unit when I had a failed FW upgrade (because of the non-existent bdrom). When I put this disk in (after upgrading to MFW 3.55) it actually tried to continue updating to 3.41 even though I was already on 3.55. I believe it failed right where it starts looking for the bdrom to update firmware. Kind of surprised I didn't end up bricking. I bet it would've if the 3.41 upgrade actually finished.
So I guess that says the hdd keeps some record of the firmware update status?
Once I get a NAND flasher I might experiment with this a bit more on a unit I have with a good bdrom.