I am sorry to tell but you can't get on the bus again once you get off.
You can reserve a ticket from Shinjuku to Shimo Yoshida(almost same price). Then after your trip in Shimo Yoshida, you can take a train from shimo yoshida to kawaguchiko station( cost 330Yen).
Actually I suggest you go straight from Shinjuku to Kawaguchiko first.There are more train goes from Kawaguchiko to Shimo yoshida, , however from Shimo Yoshida to Kawaguchiko, every hour only one or two( maximum three)train goes. If you decide get off on Shimo Yoshida first, check the train timetable before you go.
Here attach the timetable you may need.
Hope this help you.