Hmm - is the machine reasonably busy? Maybe try renice-ing the index job, and ensuring that you aren't doing a lot of swapping out of the mongodb back and forth? What is the system doing when the index job is idling?
As for the HTTPS - you are probably right, I suppose. I'll add that to my todo list.
The system running biblepay-central explorer is a quite powerful VPS (I upgraded it to test if this helps), but as said, its idleing a lot. Nothing else is running there. Maybe it is a problem with MongoDB, it seems to use only one core.
A short google search shows that this is normal for MongoDB. Mhhh, not sure how to fix this.