Timing is simply make sure all the dots line up. Rotate the engine till the idler gear dots match up with the injector cam, rocker cam and crank shaft. If they all line up (you may need to rotate the engine a few times) the timing is right.
The thing that gets me is it starts fine when warm, this indicates to me that the timing is right or else it would have a hard time starting.
The fuel system, is the bleed screw on the injector pump closed? Can you add a hand primer to the fuel line? when it starts, give it a good squeeze and see if it will rev up. I doubt this is the problem as smoke is excessive not lack of fuel that i'm thinking could be an issue.
Failing that, it could be the govenor i guess. I'm just trying to think of a way that you can manually open up the throttle on the injector pump without the govenor.
The thing with the govenor, if its not working right, it would just lower the speed, not cause smoke.... It just alters the amount of fuel the pump is delivering.....
Can you look up my profile and send me an email? i have a manual for this engine, pretty sure i do. It may give you more things to try or you may see something that yours doesn't have. It will be pretty large, but i can send it to you in smaller pieces and you can re-construct it at your end.
With the injector pump, did you note that there was a spring on one end of the block? It pushes on one end of the injector pump rack. Not sure if it could be an issue, but its possible it was knocked off when pulling or putting the pump back in.