No you don't have to remove the cyl to remove the tubes just the head. You only have to remove the cyl. to remove the tappet blocks. The push rod tubes are between the tappet blocks and and head, the head pushes down on them to seal on the tappet blocks. Once the head is off you can remove the push rod tubes leaving the cyl. in place. It would be best to have someone who knows take it apart to see if they can spot the issue but that's up to you.
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