There may be less air being introduced if an air leak where the culprit. The fuller fuel tank is much easier to draw on by the system.

I would also intently have a look at the primary filter for any noticeable air bubbles in transit.

If you have overflow on the return line from the injection pump. If that line can be temporarily stopped to see if the rough idle is essentially the same.

Does that model have the somewhat notorious fuel heater that develops leaks in a lot of cases? Or is that a later or only other model exclusive?