Need expertise!

I need some help. I have a Kohler 24hp 7000 series on a Craftsman zero turn. This spring I took it for the maiden voyage mowing and ran it out of gas. I refueled it and it was missing on one cylinder. After some research I did a coil upgrade that didn't help. I took it to the local small engine repair shop where it has been for 3 MONTHS. They called to report that they changed the carb and the muffler and it is still missing and running hot. They recommended a new motor for $1,800. It has 70 hours and has been flawless and gently used. What are they missing?
Any sort of diagnostic ability
Go to another shop or take it home & allow the tech here to walk you through proper diagnostics & repair.
 
Am I missing something? How does these coils constitute an "upgrade." And why would you replace the coils if both were firing?

Flywheel key may be cracked.
I only have basic mechanic skills. When it started having issues, it seemed like it was missing. The coils that came originally are no longer available and Kohler went back to the version I bought. There was several youtube videos addressing what I thought was the issue. There was no change in performance
 
Is the muffler running hot or the engine? How did they tell the engine was hot? Does it have a temp gauge?

slomo
The shop had all the heat shields off and said the muffler would glow red after about 10 minutes. No temp gauge on the machine. I haven't picked up the machine yet as I was hoping to gain some knowledge here before refusing to pay the bill.
 
Muffler glowing red. That can be afterburning where raw fuel is burning in the muffler. Carb or dead cylinder pumping raw fuel into the exhaust. Or super lean which raises the exhaust gas temp. Kills engines too. New muffler won't fix that. A trained tech should be able to look at the spark plugs and get a feel for what is wrong.
 
I try not to second guess or bad mouth another's work but a shop should be able to diagnose the problem.
Check valve lash and observe lift then do a leakdownd test. If all that is good compression is eliminated. Check flywheel key. Check spark on both cylinders with a gap tester. If good install NEW plugs and use an inline neon tester on each plug to monitor spark while running. If that is good it just leaves air fuel mixture delivery. It's not the space shuttle. It's not that complicated. If you don't know what is wrong eliminate what you know is right till you find the problem. A place you are paying should have the basic tools and skills to troubleshoot the problem without guessing or throwing parts at it. The average Joe may not have the tools or skills or tools but a shop should.
 
Something else to keep in mind is with today's leaner running engines it is not unusual for the exhaust to get a dull red, Most likely not noticeable in daylight but can be seen in the dark or dim lit areas.
 
I try not to second guess or bad mouth another's work but a shop should be able to diagnose the problem.
Check valve lash and observe lift then do a leakdownd test. If all that is good compression is eliminated. Check flywheel key. Check spark on both cylinders with a gap tester. If good install NEW plugs and use an inline neon tester on each plug to monitor spark while running. If that is good it just leaves air fuel mixture delivery. It's not the space shuttle. It's not that complicated. If you don't know what is wrong eliminate what you know is right till you find the problem. A place you are paying should have the basic tools and skills to troubleshoot the problem without guessing or throwing parts at it. The average Joe may not have the tools or skills or tools but a shop should.

What does a bad flywheel key cause?
 
Here's an update of what was done.
Checked stator
Checked load to drive pumps
Removed both cylinder heads and replaced gaskets
Replaced intake gaskets
Checked timing key
Replaced muffler
Checked engine spark
Checked fuel pump
Checked fuel intake
Checked compression
Checked cylinder Temps

It runs identical as it did when I dropped it off 3 months ago. The only difference is I'm $260 poorer and my yard looks like an abandoned lot.

Any help would be greatly appreciated.

BTW, the shop is Sturgis ATV and small engine repair in Sturgis, SD. I do not recommend.
 
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