Your post is a nit messy and difficult to understand. But from what i have read, i wouldn't think it has any thing to do with motherboard but more with one of the drive itself. Also have you checked the bios. CD wont boot if bios is not setup for it.
Ubuntu long to load, well it's quite normal if you run it from the CD.
Also boot files are located on 1 of the drive so if you try and place the wrong hard drive for boot, it just wont do it. you'll need the CD and bios setup properly so it can boot from it first.
I would suggest:
test all drive individually to find the faulty one, setup the bios to ensure it will load from the cd first even when drives are plugged in. check all drive compatibility with motherboard. Plug in 1 drive that is working fine and boot from cd to install your OS.
once all work fine, plug the other working drives
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