Sources of short stroking are not enough energy delivered to the carrier, too much energy sucked off by drag in the mechanism, too much energy taken up by extraction, too much energy taken up by the springs.
Not enough energy delivered to the carrier - Obstructed barrel port or front sight base, poor fit of the carrier key to the carrier, carrier key screws not tight, gas tube end or carrier key opening worn and leaky, carrier gas path obstructed, gas tube obstructed, gas rings gone, large clearance between tail of bolt and carrier;
Too much energy sucked off by drag in the mechanism - Binding or rubbing carrier, binding recoil spring, carrier and hammer binding on each other or inadequate lube on reciprocating parts. You can feel this during manual cycling, both with the trigger released and with the trigger pulled;
Too much energy taken up by extraction - Rough, sticky, or out-of-shape chamber, as evidenced by marks on cases and bent extraction rims. Ammo/chamber that make excess pressure, as evidenced by pierced, cratered, flattened, or lost primers, buttons of case metal extruded into the ejector plunger hole, case head growth in firing. Dirty chamber - clean with gun solvent, then lacquer thinner;
Too much energy taken up by the springs - Extra power recoil springs and hammer springs can be too much to allow full cycling. Start with GI, and if they work OK, then play with stronger ones.
Notice how many sources there are. Eliminate the gas path problems by checking them all, put in GI springs, clean and lube everything, and try it. Look over the case carefully in a good light for bent rims, trumpet or barrel shaped bodies, signs of rough chamber, excess pressure.