i dunno, i trust shays ability to jet. i think the jetting is right where it should be for break in.
since you have the kit off, chamfer the ports. other than that those scuffs don't really mean much. probably the rings just smoothing out to the cylinder walls. probably won't happen much more. they wouldn't affect compression yet so no worries. i've seen piston/cylinders with waaaaaaaaaaaaaaaaaaaaaaaaaaaaay worse scores, grooves and marks run great with reallly high compression. i think you've just got a case of the $$$kit$$$ paranoia. i would still premix richer though, but thats just my personal bias.