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Ahh you are coming up against the same types of problems I often have, in my experiance The exact same item often isn't the same in layout / design. I had this ages back with my GF3 cooling. The original I used the four smaller holes around the GPU to mount the GPU block, these holes were part of the nvidia reference card layout. Making a replacement, mk 2 Asus cooler, on the new Asus gf3 card, (that was the same model as the first one), these holes were missing!. It's annoying and will make it hard to make any unified product to fit universally.
Had similar to this just now in fitting my 9800 pro cooler to the Asus 9800xt. ok so this is a different card version so it's to be expected but many slight component placement differences on the card, some very subtle even though the cards are the same basic size & layout meant it wasn't a quick swap over. Took me the best part of a day with a dremel to modify the cooler enough to fit including the fact the overall pcb ram chip height was a little less.
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