Currently, I have an older version of mongo, i.e 2.6 running on my system. I already have my site in production and have a lot of client data. I am planning an upgrade to mongo
As you have data from mongo 2.6, index field limitation is already fulfilled. Mongo 3.2 will restore this backup without any issue.
The other way you can upgrade your db (if you have replica set) is to replace one 2.6 member with 3.2 and wait for sync, then other one... This will give you business continuity :-)