@jborn,
Your right, i just run Chameleon Wizard and checked Mac Pro 3,1 and sure enough it generates a 11 digit serial number, i didn't know that .. I thought all OSX S/N where 12 digits., not sure what to to in that case ... I guess you could try and search the forums and see if you should leave S/N as 11 digits and make MLB 17 digits or increase S/N to 12 digits, reduce MLB to 16 digits ? ... really not sure about that as I don't use Mac pro 3,1 on any of my hacks except a really old one.
I know Mac Pro 3,1 used to work for me but i haven't tested it lately, wonder if this could be connected to the recent iMessage issues .....
I see form your signature that you have Z87 based motherboard. I have two Intel 8 series hacks here, both are using iMac 13,1 and work great, if i was me i would, set to it iMac 13,1, generate new S/N, remove nvram.uuid.plist and perform step 4 again.
When selecting a pre made SMBIOS you need to think about the CPU generation and Intel Chipset don't worry too much about graphics as you can fine tune that using the boot-loader. I use MacTacker which you can download from the Appstore for free to check out the various hardware on MAC models. Matching the Apple system type to your hardware will allow OSX to optimise itself to the features in the cpu and motherboard chipset.
Cheers
Jay