I would definitely check the timing as well. As has been said, improper (retarded) timing can cause smoke, rough idle, and missing. When you step on the throttle, the timing is mechanically advanced, so it would make sense that it would smooth out at higher rpm.
Also, where did you purchase your injectors? I've had problems in the past with buying poor quality rebuilt injectors. The engine would run great under load, and smooth out at idle after a long, hard pull. However, normal starts and idling were rough. I even had one injector leak fuel and had to be replaced. I learned from that experience that you get what you pay for.
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