Early on, he confirmed that Colt McCoy would be the first quarterback to enter Sunday's game after Colin Kaepernick departs. He would not confirm which quarterback would enter after McCoy. He also said that B.J. Daniels is still doing some special teams work, but is focusing primarily on his quarterback work.
Harbaugh also said he expects Jon Baldwin to get some snaps in Sunday's game. The 49ers acquired Baldwin on Monday, and he made his practice debut on Tuesday. It seems pretty likely the 49ers will be keeping Baldwin on the roster, but they still need to figure out what he brings to the table, sooner rather than later. That evaluation process will pick up steam this Sunday.
Vance McDonald made his return to practice on Tuesday, and Coach Harbaugh indicated that he would play on Sunday. The 49ers have a competition competition between Garrett Celek and MarQueis Gray, but even with a week-long absence, McDonald has done enough to lock up that number two tight end role.
Finally, Harbaugh said that he expects Kendall Hunter to play this Sunday. Hunter was activated off the PUP list a little over a week ago. He has been slowly working his way back in practice, and it sounds like he is officially good to go. We'll see who of Hunter and LaMichael James is first off the bench this Sunday against the Vikings.