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Unless you are pulling the heads for another reason, I wouldn't pull the heads just to do valve stem seals. Youtube will have videos on how to do it without pulling the heads. Might have to invest in a different spring compressor than the ones used with the heads off. Will be a huge time saver.
The intake and exhaust seals are different as you stated in your post. If possible I would return the set you have and get the correct set.