boss asked me to draft them a letter of rec?
It’s best to behave honestly and ethically. It seems clear to me that you’ve been acting in good faith so far and cannot be faulted for the oversight of not noticing this one guideline among the many confusing hoops the grad schools tell you to jump through. And the transgression, such that it is, seems very minor to me — after all your boss took an active role in writing the final letter, presumably fully believes in its contents, and only showed it to you because he didn’t know it was forbidden.
Now, the key to handling the current situation is to keep the ethical bar high and not spoil things now with any shady or underhanded behavior. My suggestion is therefore that you send the guidelines to your boss and apologize for the oversight of not noticing this specific guideline before. Add that he should feel free to edit his letter again before submitting it and not show you the edits if he so desires. If you do that, you will be morally in the clear in my opinion, and would not have to worry about your boss developing a poor opinion of you if he were to discover these guidelines himself at some later point.
In theory you could also inform the school of what happened. If you do I am sure they will find the explanation satisfactory. And if so you will be going above and beyond what I’m guessing 95% of grad school applicants would go to the trouble of doing if they were in a similar situation.
Good luck!