Group the list into Lists of size 2, then combine those into lists separated by the separation character:
val sl = List("1","2","3","4","5") //> sl : List[String] = List(1, 2, 3, 4, 5)
val grouped = sl grouped(2) toList //> grouped : List[List[String]] = List(List(1, 2), List(3, 4), List(5))
val separatedList = grouped flatMap (_ :+ "a") //> separatedList : <error> = List(1, 2, a, 3, 4, a, 5, a)
Edit Just saw that my solution has a trailing token that isn't in the question. To get rid of that do a length check:
val separatedList2 = grouped flatMap (l => if(l.length == 2) l :+ "a" else l)
//> separatedList2 : <error> = List(1, 2, a, 3, 4, a, 5)