RealGM

Let's jump ahead six months to the draft and see how the Niners can fill some holes.

First the free agents at the WRs position includes Boldin and Manningham.
The backend of the defense will include Tarrel Brown, Eric Wright, Donte Whitner, and maybe a cap causality Carlos Rogers. Chris Culliver should be back to normal when the season starts.
Jonathan Goodwin is at the end of his playing career.
Colt McCoy, backup qb.

Now who hasn't played well this season and could be replaced.

Guard Mike Iupati, once again the run blocking is terrific but his been beaten badly on a weekly basis pass blocking. The offensive line was a great strength last season but has been averaged at best this season.

Round 1: Jarvis Landry, WR, LSU, speedy wideout with great hands.
Round 2: Kyle Fuller, CB, VT, a big corner, with a big body and fluid hips.
Round 2: Kelvin Benjamin, WR, FSU, a redshirt sophmore, if he comes out, a 6-5 nightmare with speed
Round 3: Ed Reynolds, SS, Stanford, could he be the first Stanford player Harbaugh drafts
Round 3: Dominique Easley, DT, Florida, just like Carradine, could be a redshirt season for Easley.
Round 4: Spencer Long, G, Nebraska, another player whose season ended with injury, but is a top 100 player.
Round 4: Keith McGill, CB/S, Utah, a tweener who makes big plays
Round 5: Braxton Miller, QB, Ohio State, a smaller clone of Colin.
Round 6: Ryan Hewitt, FB/TE, Stanford, a replacement for Dixon
Round 7: Four picks total, anything is possible

I like your first couple of picks, though I might flip the order and go CB in the first round (Verrett or Ekpre-Olomu) and WR in the second (Matthews, Robinson, Beckham Jr?). Really like the Reynolds pick, I think he would be an upgrade over Whitner and give us a pretty beastly safety combo.

As far as QBs go though, I don't think Miller is an NFL passer. I'd rather go after someone like Fales or Aaron Murray.