Here is a picture of the CPU retainer bracket before any modifications:

All of the holes look nice and round.

I marked one corner (so I was always testing the same fit) and started in on the holes with a dremel. The intent is to shift them about 1mm up. I'm not using calipers or anything at all scientific. I'm doing it all by eye. Note that this means I might have the right side fitted correctly and not the left. And I may end up over compensating. My inspiration are those oval screw holes on older hard drive brackets.

I'm fitting the lower left and upper right screws in when I'm doing my tests. I leave the screws loose and move the bracket up and down to check the fit. Here we can see the original offset:

And here we can see the new and improved offset:

At this point, I'm getting leery of making more shavings. If we look at a closeup of one of the holes:

you can see that I may end up going to far. I have no clue what will happen as I tighten the screws later. I don't want a crack.

Just by eyeballing the remaining clearance needed and the bracket to be carved off, I'm not convinced that that this is plausible. Right now I have a working bracket for the stock CPU fans and I'm flashing on the old adage, "Measure twice, cut once."

Also, I've got another problem on the daughterboard. You can see that even unconnected my test blank is not going to fit:

There is a header there (for the CPU fan) that is blocking lining this up correctly. I shaved down the outside of the retainer and got it to fit: