Certainly possible for one element of an in line injection pump to be out of proper sequential order with the others as to exact position. Thats what the adustment is for to compensate for production tollerances etc. Actually totally out of sequence is impossible. The only way that could be accomplished is swapping injector lines to the cylinders.

To find out if it is possible to be as far out as yours would have to be. I would talk to an injectioon pump shop about that.

Personally I still do not like the fact that the cylinder tests lower compression wise when the engine is hot. This is abnormal to me. I could see the same or higher. But lower?

I would do a leakdown test just to see with the engine hot and cold.

As you suggest I would still expect the cylinder to light off .In fact it does until the temperature rise gets going. It may be a total waste of time but I still would want to critically inspect the valve train for that cylinder. As Mr.Hunter alluded to it could be just a head gasket as well. The leakdown test may help there.

Really though things are not adding up well here. If you are determined to check out the injection pump you may live in an area where a cheap one from a pick and pull is an option. The pump shop may or may not be reasonable in cost. Although you could also talk to them before taking it in. One certainty is the compression lower when hot will not be changed.

I was sitting here trying to frame an example of one possibility. At say 60 degrees the compression is 400. At less than 200 degrees it drops to 300. Is there not a probability that the heat of combustion or compression takes the cylinders compression way lower?

That heat of combustion/compression is multiples of the temperature and pressure spread you are observing. You have to consider that the heat of compression alone at higher revolutions may take the cylinder pressure down further .

The fact that the #2 cylinder seems to run well when first started up cold indicates to me the injection pump may still be fine. The exception being the delivery valve seals on your type injection pump can be a little flakey. I am getting way beyond my knowledge depth here though.

I assume you have checked for any bubbling in the coolant when the engine is up to temperature? And done the upper coolant hose test the next morrning? The hose should be flacid the next morning. If it is still very firm definatly forget the injection pump. I really would forget the injection pump for now anyways. You have enough fish to fry with the falling compression.