According to Matt Maiocco of the Press Democrat, the following is the draft order for the 49ers.

Round 1, No. 29, Overall 29 (from Indianapolis)
Round 2, No. 8, Overall 39
Round 3, No. 12, Overall 75 (from Chicago)
Round 4, No. 8, Overall 107
Round 6, No. 8, Overall 174
Round 7, No. 7, Overall 214