The log output when a replica set has completed the initial clone and is now running through the oplog is not very detailed. E.g. I had no idea what was happening for 25 minutes here:

Thu Dec 16 07:45:55 [replica set sync] replSet initial sync cloning db: admin
Thu Dec 16 07:45:55 [replica set sync] replSet initial sync cloning db: test
Thu Dec 16 07:45:55 [replica set sync] replSet initial sync query minValid
Thu Dec 16 07:45:55 [replica set sync] replSet initial sync initial oplog application
Thu Dec 16 08:09:34 [replica set sync] building new index on

{ _id: 1 }

for postbacks.postbacks
Thu Dec 16 08:09:35 [replica set sync] done for 108421 records 0.465secs
Thu Dec 16 08:09:55 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 187ms
Thu Dec 16 08:10:01 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 180ms
Thu Dec 16 08:10:08 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 127ms
Thu Dec 16 08:10:11 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 330ms
Thu Dec 16 08:10:35 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 109ms
Thu Dec 16 08:10:39 allocating new datafile /mongodbdata/sd.2, filling with zeroes...
Thu Dec 16 08:10:39 done allocating datafile /mongodbdata/sd.2, size: 256MB, took 0.244 secs
Thu Dec 16 08:10:44 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 206ms
Thu Dec 16 08:10:45 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 187ms
Thu Dec 16 08:10:46 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 136ms
Thu Dec 16 08:10:50 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 136ms
Thu Dec 16 08:10:51 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 187ms
Thu Dec 16 08:10:54 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 188ms
Thu Dec 16 08:11:01 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 114ms
Thu Dec 16 08:11:03 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 169ms
Thu Dec 16 08:11:11 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 120ms
Thu Dec 16 08:11:18 [replica set sync] replSet initialSyncOplogApplication 100000
Thu Dec 16 08:11:21 [conn3] query admin.$cmd ntoreturn:1 command:

{ serverStatus: 1 }

reslen:1181 211ms
Thu Dec 16 08:12:01 [replica set sync] replSet initial sync finishing up
Thu Dec 16 08:12:02 [replica set sync] replSet set minValid=4d09c3b3:af
Thu Dec 16 08:12:02 [replica set sync] building new index on

{ _id: 1 }

for local.replset.minvalid
Thu Dec 16 08:12:03 [replica set sync] done for 0 records 0.074secs
Thu Dec 16 08:12:03 [replica set sync] replSet initial sync done
Thu Dec 16 08:12:04 [replica set sync] replSet SECONDARY

It would be useful to output more about what is happening and the % complete.