1999 arctic cat zl 500 rebuild

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Q: I have a 1999 ZL 500 EFI with around 5,300 miles that I burnt the PTO side cylinder down on over the weekend. I am looking for some advice on standard/best practice as I go about the rebuild. I pulled the head last night and this is what I know so far:
  • It appears to have melted down due to a lean burn on the PTO side. I noticed it was down on power when riding, and upon shutting it down, the spark plug and top of the piston were white. Also, when I pulled the head, it looks like the piston had a hot spot that melted right near the intake port closest to the throttle body.
  • It appears that a ring was broken and debris from it got slammed around in the combustion chamber for a bit.  Definitely will need a new cylinder as it is pretty badly scored. Also will need a new piston and head.
  • Mag side cylinder looks good. I have yet to check the crosshatch closely, but everything was clean with no noticeable (to the eye or to feel) grooves or major wear.
I have rebuilt several old snowmobile engines and other small engines, but have never dealt with EFI or coated pistons. Here are my questions as far as proper procedure from here:
  1. Can I just replace the bad cylinder with a remanufactured/replated one, or should I replace both so that they are both fresh?
  2. If I do not replace the mag side cylinder (the “good” one), should I at least have it honed? How careful do I (or a machine shop) have to be about burning through the cylinder coating?
  3. As long as I am in this deep, I plan to split the case and check out the bottom end for shrapnel. I will definitely replace the seals, but is it necessary to replace bearings (crank and/or rod) as well?
  4. I am going to replace the pistons and rings on both cylinders. Are there any aftermarket companies that are particularly good or bad? Take into account that this is my backup machine and I am really looking for a just a budget-conscious, reliable setup, not a fancy high-performance race setup.
– abaker262
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