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Hmm ok, did you hear three chimes when resetting the PRAM? (Just asking...)

Some other suggestions...
Reset the SMC.
Disable the firmware password if set.
If you boot up from some PCIe controller, attach the boot drive to the internal SATA2 controller.
If you are on 10.9, try the update with 10.8 or below.
Try to flash the original 4.1 Firmware from Apple. (Sounds silly, but you never know...)
Remove all "unnecessary" cards.
Get/lend an EFI GPU card.

For now i'm out of ideas, hope you got it working.
 
I wonder if it has to do with 10.9. I'll try and create a quick install of 10.8 on a USB drive and try it from there.

I do wonder if it's normal to hear the "bong" when restarting after holding the power button? I shut down, wait a few minutes and then start it up.

While holding the button, I wait for the light to flash and then release. A few seconds later, I hear the long tone. After the tone ends, I hear the "bong" as if it's restarting from there and wait a few minutes for it to restart. I don't know if it's actually updating the firmware or not.

A very generous and aweosme member is hooking me up with an OEM Mac 8800GT so I'll be able to see what's going on with the firmware updating now. :cool:
 
Reset PRAM a few times and ran the utility again a few times and still no luck getting the firmware flashed to 5,1 :( I have the MP41.0081.B07 boot rom so it's not the refurbed one with different firmware.

I hate looking at this 3690 that's sitting on my desk doing nothing lol.

Tried running the updater as root? I did the 4,1 to 5,1 flash under 10.9.1 and had no problems. Running as root could eliminate any file permission shenanigans. Make sure you follow the instructions the flasher displays exactly.

Edit: Doubt it if you're hearing the chime. Very strange!

Also, I purchased the exact CPU linked in the OP, installed it last night. Works perfectly:

Code:
W3520:
GB2 32-bit: 8472
GB2 64-bit: 9622
GB3 32-bit: 1963 single 7308 multi
GB3 64-bit: 2122 single 8241 multi

W3690:
GB2 32-bit: 14345
GB2 64-bit: 16287
GB3 32-bit: 2628 single 14513 multi
GB3 64-bit: 2837 single 16209 multi

MP 4,1 flashed to 5,1 with 48GB of RAM (3x16GB) and a GTX 680 2GB flashed with the eVGA Mac firmware. Very very happy with this system, expect to keep it for years to come.
 

Orange, you need to make your MP as vanilla as it can be before flashing: no add-on cards and EFI graphics card. Will work this way. EFI flasher does not like non-Apple hardware. Never tried it with 10.9, but 10.6-10.8 works for sure, did it may times.
Release the button right after LED will start to blink (before the tone).
 
Orange, you need to make your MP as vanilla as it can be before flashing: no add-on cards and EFI graphics card. Will work this way. EFI flasher does not like non-Apple hardware. Never tried it with 10.9, but 10.6-10.8 works for sure, did it may times.
Release the button right after LED will start to blink (before the tone).
Yeah I removed everything, GPUs, HDDs, All USB devices. Still nothing.

Don't know why that immediately after the long tone, it sounds like the Mac restarts with the "Bong" sound. It does it every time so I don't know if that's normal or not.

I'm giving up until I get a Mac GPU to see what's going on. Thanks all for the suggestions.
 
Update: Got the W3690 and installed it in my 5,1 and everything is working great with 48GB RAM for over a week. The only thing is when I hit the power button it takes like 7-9 sec to hear the startup chime and start booting but I'm pretty sure it was doing it before the proc upgrade though. Now just need the GTX680 to get here.
 
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