Where do I put the 40 days that my rental property was vacant and under repair?

Nowhere ... just enter the # of days rented or rentable even if it is not the full 365 possible. 

Nowhere. Vacant periods between renters counts for the days rented, provided you did not live in the property as:

 - Your primary residence

 - Your 2nd home

 - Your vacation home

 - Any other "personal pleasure" use.

So more than likely you will still be indicating the property was rented "the whole year" and the property was 100% business use for the entire year.