1964 cat 955h

Black smoke is insufficient air or excess fuel. Seems you have a governor problem or possibility of the fuel rack sticking.

If the fuel filters were that bad.
What shape is the air cleaner?
I do agree that it could be a sticky governor or a sluggish rack.

The air filter and pre filters were pretty dirty so I replaced both and had to repair air intake pre cleaner due to cracks.I keep coming back to your conclusion of the sticking rail on the governer.is it something that is needing a good cleaning and lubrication or something a little more complex.thanks for the replies

I should have also mentioned that this machine had sat for several months and when I started using it it did not have this problem.it only developed after about 6-8 hours of use .another question is it seems as though it seems like it runs a little sluggish normally but when it over revs it seems like it is comparable to the 1959 d8 I used to run.it is possible that the sluggish feeling is the abnoal part and when it tries to open up it is actually normal.I am not familiar with the normal engine sound of this machine.the throttle response is more touchy during the over rev condition.thanks

I reckon it was OK when you started work but some of that crud you have cleaned out has gone through and damaged the injector pumps causing one or more to stick and not allowing full rack travel, but when the rack does flip foward it goes hard against the stop and stays there until the governor spring can muster up the strength to pull it back again.
Check the air cleaner and turbo first, also the fuel/air ratio control and supply pipe, if this is partially blocked it can give similar symptoms, (OM will confirm if a fuel air ratio control was fitted on the 955H, I think it was), but I reckon you will finish up taking the injection pump to a pump shop.

I think I would retrace your steps ,take the fuel supply from the tank off at the primary filter at the transfer pump ,and make sure your getting a good unrestricted flow from the tank .Could be a problem with the tank cap air vent or blockage ain the line or shutoff valve .Recheck the primary screen to see if it is reclogged . run engine at idle and loosen each fuel line at the injector at head ,and see if the injectors are getting and good supply of fuel .
Check air ratio air supply line to see if it leaking manfold sucksion air,you can squirt either on that line ,and if engine speed increases ,it would be a indication of an leak .remove air ratio valve and squirt penetratin oil in it ,and work the valve buy pulling the stem back and forth compressing the spring to see if its working freely against the spring .There still may be a air leak at the diaphram ,may be a good idea to replace the diaphram . Before I removed the injection pump ,I think I would try running the engine with out the fuel ratio valve by removing the valve and temporaly pluging the hole in the back of the governor ,and pluging the air suckion line this would at least isolate the fuel ratoi valve being the source of the problem.

I keep going back to your first comment that it seems to do it more when on an incline. Up or down? Not sure but if it seems to do it more when on an incline I'm wondering if the governor lags and then kicks in when the engine lugs more and then over revs before it backs off if the governor is sticky. Does it seem to do it under load when on a flat surface?

Don't forget that the fuel ratio plunger is connected to the rack so if its hanging up or the manifold pressue is not pulling the ratio valve back its going to interfere with the engine getting fuel or being sluggish I have seen this problem yrs ago

The 955H (60A series) does not use a fuel/air ratio controller.