Okay the Motherboard is
definitely bent. I tried with the low weight Stock Cooler and the ports still don't align. Any thoughts about running a PC without the I/O Shield Plate? Dust? Risk?
Or could I put it back straight by screwing the mobo in the case without a cooler and letting it adjust through time?
Does the stock cooler mount with pushpins? If you still have to use screws to mount the cooler then I'd still take a guess that its to much torque on the screws, but if not then my next guess(before blaming a truely bent mobo) would be that something is catching on the motherboard right where it meets the I/O plate. Even if the motherboard is slightly bent I would think that the screw that holds the mobo to the case would be enough to force the mobo to straighten out, which is why I'm thinking something is catching on the mobo.
Maybe one of the gold(colored) spacers isn't fully screwed in? I don't know just more guesses since I really would hate to blame a bent motherboard on that huge bend.
In any case if you don't figure it out then there really isn't much to worry about running the pc without an I/O shield, just be careful when plugging stuff in so you don't accidently short the mobo with a piece of metal. I ran my last pc without an I/O shield, and the worse that happened was dust building up around the ports since it was like an air exhaust without the shield. I'm going to guess there are technical reasons for the I/O shield, such as maybe EMI shielding, but I don't worry about it that much especially since I'm running my current pc with no side panel