Welcome!
1. Some folks call this "fishbite" and is a common occurrence. I have not found a cause or solution. Mine used to do it, but now that I think about it, it hasn't happened for quite some time now. It may have disappeared when I replaced my IP a couple of years ago. Your smoke and miss at cold start is probably not related, but is most likely due to a faulty glow plug or two, or perhaps slightly low compression in one or two cylinders.
2. Your ECM is most likely defueling due to a lack of boost control. The ECM is very sensitive to boost, and tries to control it through the vacuum-operated wastegate control system. Wiring the wastegate shut will make the problem worse, since the ECM can't control the boost, and will then go into Limp mode. There are a few ways around this issue. The first way is to make sure the entire boost control system is functioning properly: good vacuum from the vacuum pump, good wastegate solenoid valve, and no leaks in any of the vacuum lines. What I did with mine was ditch the vacuum pump, installed a Turbomaster manual wastegate control, and installed a chip into the ECM from Kennedy Diesel to keep it from going into Limp mode. Works awesome now.
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