Dear Friend,
OM SAI RAM,
you mya book any hotel near shirdi temple at any time. the hotels will be available. you have to pay around Rs. 500/- per day for a good hotel. Shirdi sansthan will also provide accomodation but since you are visiting with your family so it is better to get a private accomodation behind the main temple. there are a lot of hotels behind the shirdi temple where you can get accomodation without any difficulty or approach.
it will take around 7 hours to reach pune from shirdi. so you may either take luxurious private bus from shirdi to pune or you may take train (please check the train schedule) from Kopargoan.
anything more you want, you may write here.