Limited Answer, hope it helps.
The 6.9L Ford (International) Diesel engine has that Elbow on the stanadyne pump (for the return line) that has the glass check valve in it. You need that valve in place for the engine to run properly. That valve can cause more problems than you care to know about if its acting up or dirty/clogged. Causes smoke, idle issue, lack of start, rough engine, stall, etc etc. Worth checking out.
EDIT : ok, so my roommates had me distracted and I listed the above before I forgot about it, and it was already covered. Now, let me tell you about my truck. You can see pictures of it I just posted today in a new thread. My truck had the very same behavior as yours until I put an electric pump in it with a see-through fuel filter. My fuel lines have holes in them. When I start my truck you can see a solid stream of bubbles come from the main fuel line that goes up to the separator filter. The electric pump boosted my pressure and cured pretty much every issue I had. My check valve was clean, injectors good and dry, EVERYTHING. The pump and lines and filter cost me right at 75 bucks. If you check out my new thread, look at the engine photo at the brake reservoir. you can see the green pump, fuel line, and barely see the filter over by the fuel-water separator. As this was/is my problem, I would suggest looking into it. The engine behavior and smoke are the tip off considering the amount of troubleshooting you have already done. And don't forget, the 6.9L (Ford) International is a CLOSED LOOP fuel system that cant take air as the indirect injector's need the fuel pressure to function/open.