Hi Binai,I would personally suggest departing earlier - maybe the 0540 Shivshahi from Shivajinagar. You can enter the queue earlier if you reach early. If you have a confusion with the boarding points, I would simply suggest taking cab (ola/uber) to shivajinagar (I think buses depart from Wakdewadi temporary bus station now) and board the bus from the starting point itself - its much better than having to search your boarding point midway.
I would suggest sticking to MSRTC than any of the private operators - MSRTC is known to stick to timings and will not waste time en route scouting for more passengers.
The Wakdewadi bus station is the new Shivaji nagar bus station. It is not a temporary arrangement. The new bus station in Wakdewadi is fully functional now, with auto's and PMPML buses having a dedicated stop at the place.