Just for info. I (FG649 with 4D3 pre common rail engine) had some overheating problems in Turkey due to a combination of low grade fuel, higher speeds, steeper longer hills and higher air temperatures. Radiator cap replaced helped. Different engine, no misfire.
I'd suggest replace the thermostat. If nothing else the engine running cold can change the symptoms from other problems.
You are now at 1360m above sea level though far from the level where the electronics will complain (about 3,500 - 4,000m). But may be sufficient to effect a fuel system that was marginal but working at lower altitude.
Recollection from a long time ago is there's a mesh filter on the end of the suction pipe in the fuel tank. Unlikely a problem but.... The two pipes, (supply and return) and fuel gauge sender are removed by undoing the six or so screws around them on the tank (assuming standard tanks).
I suggest tighten the hose clips on the fuel supply pipe at the fuel tank. Screw clamps are better than the original spring clamps. A very small (pinhole) air leak can be enough to reduce fuel supply but not enough to collect air in the fuel filter. Though it tended to just slow my engine down until it stops rather than misfire.
With some dual tank instals with changeover there can be a small pressure drop across the junction which requires an extra lift pump to overcome.
At one time I put a temporary pipe direct from fuel tank to fuel filter which allowed me to isolate a fuel line problem. There's a wonderful auto parts place in Ulaan Bataar just where the main road west through the power stations leaves the main road north that has more sizes of fuel line than I've had hot dinners.
Big silly question. Does the engine behave the same way with both fuel tanks ?????????? Did the biodiesel get into both tanks? Were both tanks ever filled at the same fuel station (I avoid that where I can). Flushing one tank and refilling can provide a way of isolating fuel supply as a problem.
Valve clearances.
A bit early and I'm a bit reluctant to suggest a cylinder compression test.
I have 2 aftermarket fuel tanks. The mechanics don't think it is a fuel leak otherwise air would've been coming through the lines. I haven't had any problems with tank changeover until now. The engine does behave the same way with both tanks and biodiesel was in both.
A complete, (and very expensive) fuel system change is on the cards at the moment.