The motherboard is linked to the logic board in a way that they talk to one another and if they are not paired they will not work so to speak.
As long as the connectors are the same you can fit different boards but you will still have to re-marry the 2 boards together and you will have to be on 3.55 or below to do this.
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Found this so have a read and see what you think.
http://www.ps3hax.net/2012/03/ps3dev...firmware-3-55/