[mykwyner]

I wouldn't use in for the past because in means at some time inside of a particular time period. Since it is the past, you know the exact time he came back.

He will come home in a couple of days. (future)
He came home after a couple of days. (past)
He came home in a couple of days. (past)
He is home after a couple of days. (present)
He will be home after a couple of days. (future)
He will be home in a couple of days. (future)
He was home in a couple of days. (past)
He was home after a couple of days. (past)

The real difference, as I said earlier, between in and after in these sentences is when, during that period of a couple of days, did he come home.

Note: I was unable to use in a couple of days in the present tense.