Only about 89 miles on the break in. I read somewhere that before the rings are seated emissions could be higher. I had a shop put in the engine, I added fresh gas to the tank before I dropped it off at the shop. It didn't sit for the whole 1.5 I would run it periodically. Probably would have been a good idea to drain the tank, but that didn't happen. The truck was run several times after the tank was filled with the fresh gas. So it was mixed with the older gas.
There are a good number of differing opinions and procedures for breaking in these engines. It's my opinion that 89 miles (that is maybe 2 hours of run time) is not enough time to completely break in these engines. It's likely that a fresh engine rebuild without at least a 1,000 miles on it may not pass emissions, depending on what state is testing.
Gas can go bad in 3 to 6 months, and ethanol-based fuel is more likely to collect moisture. After one fresh tank the old gas should be gone.
What is the break-in procedure that 22RE Performance suggested?
Has the engine been re-checked, especially the sensors, and tuned?
Gnarls.