After all the documents are fetched by Server2, It starts making secondary indices. It takes around 3 hours for indices to get finished.
At having received a timeout error it (Server2) simply drops all databases and starts the initial sync again.
The snippet from logs is below:
2016-05-25T11:50:36.053+0000 I - [rsSync] Index Build: 2211700/2215091 99%
2016-05-25T11:50:39.221+0000 I - [rsSync] Index Build: 2212000/2215091 99%
2016-05-25T11:50:43.300+0000 I - [rsSync] Index Build: 2212300/2215091 99%
2016-05-25T11:50:46.103+0000 I - [rsSync] Index Build: 2212500/2215091 99%
2016-05-25T11:50:49.068+0000 I - [rsSync] Index Build: 2212800/2215091 99%
2016-05-25T11:50:52.218+0000 I - [rsSync] Index Build: 2213600/2215091 99%
2016-05-25T11:50:55.439+0000 I - [rsSync] Index Build: 2214500/2215091 99%
2016-05-25T11:50:58.738+0000 I - [rsSync] Index Build: 2214700/2215091 99%
2016-05-25T11:51:13.223+0000 I - [rsSync] Index: (2/3) BTree Bottom Up Progress: 536600/2215091 24%
2016-05-25T11:51:23.285+0000 I - [rsSync] Index: (2/3) BTree Bottom Up Progress: 1984500/2215091 89%
2016-05-25T11:51:24.317+0000 I INDEX [rsSync] done building bottom layer, going to commit
2016-05-25T11:51:24.508+0000 I INDEX [rsSync] build index done. scanned 2215091 total records. 10491 secs
2016-05-25T11:51:25.082+0000 I NETWORK [rsSync] Socket say send() errno:110 Connection timed out xx.xx.xx.xx:27017
2016-05-25T11:51:25.106+0000 E REPL [rsSync] 9001 socket exception [SEND_ERROR] server [xx.xx.xx.xx:27017]
2016-05-25T11:51:25.106+0000 E REPL [rsSync] initial sync attempt failed, 9 attempts remaining
2016-05-25T11:51:30.106+0000 I REPL [rsSync] initial sync pending
2016-05-25T11:51:30.433+0000 I REPL [ReplicationExecutor] syncing from: xx.xx.xx.xx:27017
2016-05-25T11:51:30.563+0000 I REPL [rsSync] initial sync drop all databases
2016-05-25T11:51:30.564+0000 I STORAGE [rsSync] dropAllDatabasesExceptLocal 42
2016-05-25T11:51:31.925+0000 I JOURNAL [rsSync] journalCleanup...
2016-05-25T11:51:31.925+0000 I JOURNAL [rsSync] removeJournalFiles
2016-05-25T11:51:32.331+0000 I JOURNAL [rsSync] journalCleanup...
2016-05-25T11:51:32.332+0000 I JOURNAL [rsSync] removeJournalFiles
2016-05-25T11:51:32.489+0000 I JOURNAL [rsSync] journalCleanup...
2016-05-25T11:51:32.489+0000 I JOURNAL [rsSync] removeJournalFiles