The pictures make it look like you are even blocked from getting the CPU cooler to sit down flush over the VRM block....yes? If so, I think that is your bigger issue.
I think the chipset block holes will work fine between slots #1 and #3. If you can actually fit a card in slot #2 while your classy is in slot #1, then I don't believe you will have an issue with extender fittings on the chipset block. Probably can't use compression fitting though.
But it really looks like your CPU cooler bracket is going to cause issues no matter what you do. May be time to start looking around for another CPU cooler....