Thanks @drvbs .Hello
The 6:30 a.m NEETA ( then Merc or Volvo, not sure what make now ) used to reach Shirdi only by 11:30. I would suggest you to take the 5:40 a.m MSRTC Shivshahi ( Pune--Amalner via Nagar--Shirdi) from Wakdewadi bus station, Pune. Presently, some part of Nagar--Shirdi route is in a bad state, thanks to the apathy of officials and politicians concerned with this region.
Hope situation will get back to normal in a week time else will cancel the plan due to uncertainty. If I continue my trip will update the details here for sure.
Thanks to all for your suggestions.