I started by replacing the pedal shaft on the brake pedal. It had work from years of use as shown in the picture below. I purchased a replacement shaft from CJ Pony parts a few days ago. The original had a tab which was press fitted into the brake pedal assembly and then hammered so it would flare out and not come lose. I welded the new one in place.
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I used a wire wheel to remove all the old paint and surface rust from the pedals. Once they were ready for paint, I covered them in Rusoleum Rusty Metal Primer and then Krylon Satin Black paint. They turned out looking pretty good.
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You will notice the actual pedal portion of the assembly in the picture above is different. I used rubber pads in the past which slide over the metal pads. The clutch one always falls off. I've used a few different things to glue it on but nothing works very well. I had some adhesive black grit paper which is normally used on stairs. It is really thin so I cut some to fit perfectly on the pad faces. I'll likely use them like this at first and if it does not work out, I can always reinstall the rubber pedal covers.