1 = Had Come Talks about an Action ( in this sentence "come") which has happened before another thing in the past.
Example for Had come : Imagine a situation in which 2 things have happened and we're talking about them :
1 = I did my homework ( at 9 PM)
2 = I watched TV ( at 10 PM)
5 Hours later i want to report these things to my Mother :
Me :Mom, I watched TV at 10 !
Mother : what about your homework ?
Me : I had done my homework before i watched TV.
2= came Talks about an Action which happened in the past and IS NOW FINISHED. and we're not talking about any other action.
3 = used to come is a different Grammar which talks about an activity that you regularly did in the past and no longer do (it) now.
Example : I used to smoke ( Means : In the past , smoking was a habit of mine and it no longer is)
The Main Source of the answer is Cambridge Advanced Grammar in Use(Third edition)