Which storage engine are you using, WiredTiger or MMAPv1?
--WiredTiger

Can you please post the output of db.messages.stats()?
-- Please see messages-stats.txt

Can you please post the output of db.collection.getIndexes()?
-- Please see getIndexes.txt

Can you post the document that was inserted 4 million times?
-- Please see sample_doc.txt

Did you set any options during the mongorestore?
--No

Can you post the output of the following?
db.messages.explain("executionStats").find({$text:{$search:"terribly"}},{"body":1}).limit(2)
-- There are four output for terms terribly and Unfortunately.