An easy way to trouble shoot the 6.2L with a miss/rattle is to get the engine to normal operating temp, and with the engine running, loosen one injection line at each injector one at a time to determine if "killing" that cylinder makes a difference (similar to pulling a spark plug wire on a gasser).
For example, if "killing" the injector makes no difference to the engine running, then you have found your dead cylinder. However, if that process causes the engine to miss and run worse, then you can move on to the next cylinder. This also applies to the noise. If "killing" the injector causes the rattle/knock to go away, you have found your suspect. This can then narrow down further diagnostics needed for that particular cylinder.
Once you have found a particular cylinder giving you the trouble, another easy check is to swap injectors with a known good cylinder. If the problem follows the injector, you know you have a faulty injector. If it remains with that cylinder, then your issue lies internally.
I had a 6.5L once that was running really rough. This process quickly led me to a problem with cylinder # 1. A follow up compression check found almost zero compression on that cylinder. Turned out to be a broken piston.
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