cat 3116 fuel turning black

Fuel will turn black if it is overheated too. Low flow in the head, low pressure. Yes, if combustion is getting through you will get those symptoms.

 

You are getting combustion leakage past the injector seats. That is why it misses upon start up. They use copper seats and they have a tendancy to leak past the bottom injector seat and destroy the seals. Only someone who knows what is going on, should pull the injectors and re-ream the seats and check for combustion leakage damage to the bottom injector seat area. This is a common problem with 3116's. It will not effect the fuel pressure. You may see a lot of air in the return line.

 

KGKTM: The seal according to CAT is a secondary seal if the beveled edge of the injector actually seats in the cup with a 360 degree seal as it seats in the cup and cuts into the copper sleeve. Every time you pull an injector the seat needs cut and if removed and cut enough times the cup will need replaced. We used to use a spray machinist blue inside of the cup after cutting the seat and renewing it and verified the seat was perfectly cut, even, and sealing 360 degree pattern. I just got proficient and did not need the bluing to verify. Glad you found it.