You can use one of the commercially-available flushes like mentioned above for the cooler and lines. Are you running the OEM cooler in the radiator only or do you have an external one by itself or along with the radiator? If external, it is pretty easy to remove and clean out. Sometimes sediment can settle in coolers and it is almost impossible to remove all of it. As for the converter, find a local trans shop that has a flush setup for that.