Reaching Bodhgaya from Gaya junction auto is the best mode of travel. Autos are available outside Gaya junction. During our travel we upon arrival booked entire auto for Rs. 200 though auto driver was asking for Rs. 250 but upon bargain he was ready for Rs. 200/-. No extra charges for luggage. It was comfortable journey as road condition is Ok.
During return journey via auto from Bodhgaya to Gaya we discover auto fare is Rs. 25/- only if we opt for sharing.
Thus, the conclusion is to reach Bodhgaya from Gaya Junction or vice versa one of the best mode of travel is auto. Sharing or not upto you. The journey time is approx. 45 minutes but you should start little early because few times there is traffic on road.