If there is another solution to change it, I don't know of it. You can also quickly highlight the portions in the message body you don't want and delete it. I find it works about as well and fast as selecting specific text depending on the message and what I want to keep in it.
For rules, remember that they apply only to new incoming messages to the Inbox. If they are read on another device first, then they will download to the computer where the rules reside and be shown as read. The rules won't act upon them. Also remember that rules are applied in the order of the list. Make sure no rule above or below affects message rule that isn't working like you expect.
For iCloud vacation response, that is set at the website. If you have problems with an iCloud account, maybe something got corrupt. The only action to fix that is to sign out of iCloud via system preferences. This will remove the account from Mail and will remove the files from the computer. Signing back into iCloud will recreate the account and fresh files on the computer. It usually fixes any iCloud problems.
Good Luck