Mac Pro - Early 2009 - 4,1 wont boot under OSX
You have moved drives around, what about memory? Set it up with the minimum memory, then try with other memory modules, maybe you have a bad stick or two. Maybe one of the memory daughter cards is bad. Swap those, will a MacPro boot without an (empty) daughter card? Not sure about that

Also try unplugging the Optical drive.

You tried the Video card in another slot. How about another video card?

Anything that can be removed, should be removed to see if it is at fault.