I notice the exact same symptoms with my '95. If you recall, I replaced the IP back early this spring with another used pump. She runs great, but the first morning starts are funny. Especially now that it is getting colder out.
This morning took a few seconds of extra cranking, and then she started, but had very little diesel rattle, and lots of white smoke. Then a second or two later, the diesel rattle becomes very evident, and the smoke goes away. I can tell that the timing is not advancing until AFTER the engine has started. I don't know if the stepper motor is sticking, or if the ECM is not telling the stepper motor to advance the timing prior to starting. I didn't have this issue until after I swapped pumps. And I did perform a TDC offset relearn with a Tech II scanner after replacing the pump.
I'm not sure where to go with this one, but it sounds like you and I have the same symptoms. And I believe it is directly related to swapping the injection pumps.
Casey
1995 K1500 Tahoe 2 door, 6.5LTD, 4L80E, NP241, 3.42's, 285/75R16 BFG K02's; 1997 506 block; Kennedy OPS harness, gauges, Quick Heat plugs, and TD-Max chip; Dtech FSD on FSD Cooler; vacuum pump deleted, HX35 turbo, Turbo Master, 3.5" Kennedy exhaust, F code intake; dual t/stats, HO water pump, Champion radiator; Racor fuel filter