Definitely NO LEPTO for these little guys. My vet recommended that I do the regular shots and then a week later do the rabies. Reactions are relatively rare, They most likely will be groggy for the rest of the day and just nap and they may get a little bump where the shot was administered. I'm not sure about anything different for the cleft palate pup.
Please remember that despite what anyone will tell you about the negatives of vaccine, it is a widely used and generally safe practive and it's always better to be safe than sorry.