Had the same brake problem on my customer's (Eagle) kart. First you want the 3/16" thick MCP rotor. It's a little bigger in diameter too. You will need a 1/16" spacer that Comet sells to go in between the caliper halves.
The rotor should engage the whole brake pad. There are adjustment holes drilled in the caliper mounting bracket and they usually don't line up with anything. The fix is to take a rat tail file and drift the holes to where you need them. Next you need a thick grade 8 SAE flat washer under the head of each caliper mounting bolt to bridge across the crappy mounting holes. Even if you don't file the holes you need the thicker washer because you're still bridging a slot. With the washers and the spacer, you may have to use safety wire on the nut side instead of a cotter pin on the castle nuts. Since your brake pads have a step in them, you'll need new pads.
Now the bolts that hold the disk onto the hub were only grade 5, metric thread, not drilled for cotter keys and they have no shank. I replace mine with grade 8 hex head 5/16- 24 with 1/2" shank and all 4 are drilled for a 3/32" cotter pin. The nuts are all metal grade 8 crimp nuts.
The clevis pins on the brake rod have no washer under the tiny cotter pin. This is prone to fail, and the pin will fall out. Seen it more than twice and it usually involves a helicopter ride. You need longer clevis pins that use 3/32" cotter pins and are long enough to have a washer between the cotter pin and the clevis fork. I use a 1/4" grade 8 hex head bolt with a long shank to make mine. Also please keep the legs of your cotter pins short (1/4"). I see too many long straggly cotter pins that just vibrate and snap off leaving you with no brakes.
Hope that helps,
Sundog