So should I put in without the head on? Wouldn't it be easier to line the tranny up to the engine without the head on?

install a fully assembled engine. minus maybe the exhaust manifold

With or without the lift hooks on the head? If not with them then where do I bolt the chain?

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I also have a engine leveler. Will it clear using it?

gonna have to play with it. we arnt there to manage it. you have to leave the hooks on it thats why they are there.