Rough Idle on truck partially sunk..

Hey guys I got 03 Chevrolet Silverado that hasa 5.3l in it Vin t.. not flex.. doesnt have egr on it.

last summer i was offroading when i nose dived it into a water hole and got stuck cause it bogged out. had about a foot of water in the cab while it idled (not the greatest) under water for over an hour.

while sunk i was low on gas so i added a jerry can while it was idling under water.. got pulled out backwards and water splashed up under the dash.. while limping it home it slowly lost power and died was also stuck in 4low as i have the auto 4x4 option..

once i got to working on it to get it running again i first pulled plugs and drained oil.. cranked it over with no plugs to make sure cylinders were dry and also sprayed them with seafoam.. i cant recall exactly how it got running again but i know i did new plugs, oil.. pcm? (was a noob and thought it might be fried)..original pcm is back in.. anyways ran like crap untill i unplugged my upstream o2s and it calmed down and got better..

at this point the truck drives as my daily with 140000km on the clock..still has a slight rough idle and was having long cranking issues hot or cold intermittently..

parts ive changed

new ngk wires
3 new sets of plugs both ac delco iridiums and atm ngk iridiums
new fuel pressure regulator (helped at first with long crank but still had some here and there)
new felpro intake gasket and injector orings
new ac delco upstream o2s..gave inactive code so put in used denso sensors
gutted my cats as one was rattling and added rear or extensions to avoid codes
put in a used crank sensor off parts truck
newer maf and map (removed a p0101 i had before i sunk it)
throttle body off low milage truck that worked..
shop checked maf ground and did crank relearn...
new ac delco fuel pump..filter and fuel lines and evap line all the way..
swapped a used injector in #6 as i was losing fuel pressure.. so far no long cranking since swapped.. also swapped evap purge solonoid for used one off parts truck and reinstalled the fuel pressure regulator as when i first did so i think it wasnt sitting right..
swapped around some coil..no difference..

last i looked no codes and fuel trims are near perfect give or take 5%

she seems to run smooth at a cold start idle but once it goes down to 500rpm maybe 550 you can feel it stumble to a rythem if you want to call it that..

at a loose on what to do next and what to look at.. thinking maybe injector balance test and manual idle relearn through scan tool at shop?