Are you sure you got the right injection pump? Sounds like you might have one too big. A 6.2 uses a .29" pump and a 6.5 uses a .31"pump. What is the ID number on your's?
For example, this is a 6.2 pump -
DB2829-4879 10149634 1990½ HMMWV (Military) - 1.2 cSt
Note the "29" in the 5th and 6th digits. That stands for .29"
This is a 6.5 pump -
DB2831-5149 12550433 1994-96 HMMWV (Military) - N/A, 1.2 cSt (170 hp)
Note the 31 in the 5th and 6th digits. That stands for .31"
And yeah, maybe somebody took a 6.2 pump and turned the fuel up higher then it ought to be. But, that's only going to effect max fuel setting. It will NOT make it smoke badly in normal driving unless you're really working it.
On the other hand, a pump that's too big will make it smoke all the time.
In regard to timing - most people and mechanics have no way of checking it. The whole idea of lining up the marks doesn't mean much. All that does is verify that your timing will be correct when the engine is cranking or at idle speed. Does nothing to tell you if the timing is correct when the engine is pushing you down the road at highway speeds.
The Stanadyne pump has an automatic timinjg advance that advances ignition/injection timing almost 14 degrees before-top-dead-center at high RPMs. Then it drops back to no advance when idling, or just cranking it to start. So, it's easy to have a pump with the advance not working, yet you set it according to those marks - and when driving, your timing is off by 14 degrees - which is a lot.
The only ways to check timing on a 6.2s are - with a diesel timing light adapter, . . . or with a luminosity probe stuck into a glow-plug hole, or . . . with the pump off the engine and mounted on a test stand. There is another way - sort of. A timing window can be mounted on the pump -but it's hard to do with a 6.2 since the pump is kind of buried in the middle of the engine, down low.
