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Hi Adam, you stated a fresh set of Injectors. Stock injectors are a split shot, however many aftermarket performance are single shots. This causes the timing to be off and requires custom tuning to fix. IMO the best tuning is the Hydra Chip with Gearhead, Jelibuilt or another reputable tuner. I like Gearhead because yes it's a conservative tune so you won't break your stuff, they're very responsive in their emails && they offer free lifetime revisions so if you further upgrade your vehicle you can always get a revision.
If you did not go with single shots have you driven it for an extended period of time? When injectors are put in air is introduced into the system and they will run rough until the air is bled out. (Which should affect it whether you're pulling a load or not)
Your symptoms sound like you're running single shots on split shot tuning.
P.S a rough idle shouldn't damage your trans. Especially if it's the single shot injectors.
'02 F-250 7.3
180/80% Stage 2 Full Force Injectors
Hydra running Gearhead Tunes
5" Straight Pipe
Bilstein 5160 Resi's
Rough Country Dual Steering Stabilizer