I can't comment on the mechanical issues here but the ongoing issue of dealers replacing parts on the customer's dime as a diagnostic tool is something that as a practice needs to end. I've been over that a few times with car repair and got to the point of having to threaten legal action against a dealer due to their inability to diagnose a problem. From that point forward I refused future repairs unless the dealer guarantees a fix or refund of repairs that don't fix the problem. If I'm paying $170/hr labor rate I expect expertise to diagnose and repair on the first attempt. Anything beyond that is a problem and I'm not afraid to exercise my rights as a consumer.
In one case a dealer failed to repair my car after two unsuccessful attempts totaling about $2,000 and wanted third shot at it for $4,500 more. I told them to take the parts out and return the car to me in the condition I brought it to them. I told them to eat the labor cost on the first two repairs as a lesson on how they need to hold their technicians to higher standards when customers are paying. They called back and told me they'd do the $4500 repair for free.
In your case, were either the injector pump or ECU bad? If not I'm guessing you'd rather have your $6,000 than two new parts that didn't need to be replaced.