You should leave your cam covers on, their placement is crucial to your starting the auto at a later date. It's going to be easier to pull the entire tranny at the same time as the engine. I say easy but the truth is you have some work to do either way.
I lapped my block while still inside the engine bay. Because there's just no need to pull it if you can keep from it. I hope this doesn't bite me in the ass and if it does it'll be a ground zero rebuild.
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