Need help, series 60

if your problems started after running the top end, my guess is that they didnt get the lock nuts tight and your top end is all out of wack. I would have the valves and injectors re adjusted. also detroit recommends that the jake system be adjusted when the engine is cold.

 

Possibly air in fuel?

Or maybe the turbo is giving up, do you have a boost gauge?

 

Have you had the 02 sensor checked as well.
A bad and stopped up catalyct converter and/or plugged air filters will make the mileage go down as well.
A leaking injector could be a issue.
The ECU could still have codes in it, making the engine run in a closed loop or be bad.
Often over looked is the water temperture not getting to operating temp and/or bad sensor or not enough coolant.
Timing could be a problem to. Bad overhead adjustments.
Vacuum leaks, ie intake manifold or craks in the inter cooler (in front of radiator), bearings in the turbo galling up( running slower than OEM).
A possible crack in exhaust manifold and/or studs.
Hope some of this is useful. You never know anymore, just because parts are new, does not make them good. Good Luck.

 

A bad ECM and/or sensor(s). Not getting the signal to the ECM. Could Be as simple as a Bad Ground or connection or wire. Most of that fine sensor wiring underhood gets a lot of hot and cold cycles on them. Hpoe it helps and good luck

 

From what you describe, gasping for air indicates that engine is not getting enough air. Smoke in the shadows points to that as well. You need to check the fresh air side of the engine real close for issues. The miles on tractor and your shops attitude sounds like they are just humoring you till this tractor becomes your problem, instead of theirs.(still making payments).
But the issue described points to the air to air exchanger in front of the radiator. There are a lot of tubes in that exchanger some of which could be cracked, broke or stopped up and you are losing the tubo boost through the exchanger. That part needs to be pressure checked. If you can find a way to restrict the air flow into you intake manifold from the exchanger, with engine at 1/4-1/2 throttle, take spray bottle of a very soapy solution and spray the exchanger with the hood up so you can see clearly, the rows of tubes, any bubbles at all indicates a bad exchanger.
But you also said problems started after the overhead was done, by your company shop. If it was not done correctly, this is more than likely where your problem is at. You may have to go to an outside shop(dealer) and have the overhead run on it again as well as the other issues in your post. Let them tell you wether it is out of wack or not.(documentation) They also can pressure check your exchanger if there are no problems with the overhead.
The EGR tubes could be an issue as well, if the engine is starting to burn a lot of oil, your post did not say.
A (dealer) can also tell you when the recommended IN FRAME OVERHAUL IS DUE, (with a phone call) your tractor is approaching 3/4 of a million miles or more on it. In the old days a tractor had a inframe overhaul about 5-600k miles and the issue descriptions in your post, describes an engine, close to being worn out and your SHOP will not tell you that, for obvivous reasons.
The documentation will be useful if you have to take it up with the company you are buying the tractor from. These late model tractors are very complex nowadays and little things with them seem to matter a lot.
I really do hope some of what I have said here is useful to you. Best Wishes.