If you are seeing 3-400* temps on the flue pipe measured with a magnetic thermometer, you are running the MarkII near full output. The gas temps inside the pipe will be 1-200* higher. Three full turns open is essentially wide open
If you have a strong draft, you should be able to turn down the air vent in the ashpan door, [completely close the vent in the loading door!!] and get your flue temps down to ~200* and get several more hours of burn time out of a full load of coal. Looking at the photos of your chimney, you are really at a minimum for height. The problem is that the flue enters the masonry chimney about five feet above grade, so you need to subtract this from the overall height, so you really only have about 10-12' of chimney. In warm weather, with a cool fire, draft will be minimal.
Recovering a burnt-out coal fire is a slow process, the remaining coal is usually mostly embers, not really burning, but still red hot. Trying to get fresh coal to start burning from these embers can be 'iffy' at best.. Try to catch the fire when it still has some flames off the coal bed, and like coaledsweat said, open up the ash pan door, to 'rev up' the fire, add some fresh coal over the whole firebed, let it catch [lots of fresh blue/white flames] THEN shake the ashes out from under the fire.
Shaking first disturbs the air passageways around the pieces of coal, and can cause a fire to all-but go out. [been there]
Learning to be a biological stoker unit takes a bit of learning...
Does the baro damper open much when it is windy or when burning hot?? if no this is an indication of low draft.