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I would say they would work. Not sure of the HD mounts but the Kuryakyn 4562 mounts will. I'm using the HD chrome pans and floorboard inserts with the Kuryakyn mounts. These pics may help..
The mounts fasten to the footpeg hole in the frame. Looking at the pic from the side it appears the floorboard would come in contact but it won't. The floorboards and mount extend out further from the frame than just the standard footpegs. Your exhaust holds closer to the frame and the top exhaust pipe is lower than the footpeg hole in the frame. It's hard to explain. I'll take some better pics from the rear tomorrow and you can see what I'm talking about. Some of the HD mounts may differ from model to model, I'm not sure. I know the Kuryakyn mounts will work as long as your stock exhaust and brackets have been removed, which in your case they have. I'll post some pics tomorrow.
Here's a pic I found on my computer. It looks like HD mounts but I think mine are closer to the bike (don't extend out as far). I'll take some pics anyway.
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