Atf works to clean the engine. Its a detergent oil. BUT!!! I have only used it when there was a problem such as a noisy/sticking lifter. Have done it several times and has worked everytime.
As the saying goes, if it aint broke , don't fix it. If you have done regluar maintenience ie: frequent oil changes, there should be minimal sludge/build up inside engine.
Leave it alone. And be on your way.
P.S. One thing you should always flush your cooler, before installing rebuilt transmissions though.....