tm_progress.js

var assignments = {
  "Hindi-ULB" : {
    "Matthew": {
      "Milestone 1": {
        "assigned": [1,2,3,4,5,6,7,8,9,10,11,12,13],
        "completed": [1,2,3,4,5]
      },
      "Milestone 2": {
        "assigned": [1,2,3,4,5],
        "completed": [1,2]
      },
      "Milestone 3": {
        "assigned": [1,2,3],
        "completed": [1]
      }
    },
    "Mark": {
      "Milestone 1": {
        "assigned": [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16],
        "completed": [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16]
      },
      "Milestone 2": {
        "assigned": [1,2,3,4,5,6,7,8,9,10],
        "completed": [1,2,3,4,5,6,7,8,9]
      },
      "Milestone 3": {
        "assigned": [1,2,3,4,5,6],
        "completed": [1,2,3,4]
      }
    }
  }
}

var bible = {
  "Matthew": 28,
  "Mark": 16
}


function assigned(project, book, milestone) {
  var percent = 0
  var assigned = assignments[project][book][milestone].assigned.length
  var total = bible[book]
  percent = assigned / total
  return percent
}

function completed(project, book, milestone) {
  var percent = 0
  var completed = assignments[project][book][milestone].completed.length
  var total = bible[book]
  percent = completed / total
  return percent
}

function projectAssigned(project, milestone) {
  var percent = 0, completed = 0, totalChaptersInBible = 1189
  var projectData = assignments[project]
  var projectBooks = Object.keys(projectData)
  projectBooks.forEach(function(book) {
    completed += projectData[book][milestone].assigned.length
  })
  percent = completed / totalChaptersInBible
  return percent
}

function projectCompleted(project, milestone) {
  var percent = 0, completed = 0, totalChaptersInBible = 1189
  var projectData = assignments[project]
  var projectBooks = Object.keys(projectData)
  projectBooks.forEach(function(book) {
    completed += projectData[book][milestone].completed.length
  })
  percent = completed / totalChaptersInBible
  return percent
}

function status() {
  var projects = ["Hindi-ULB"]
  var books = Object.keys(bible)
  var milestones = ["Milestone 1", "Milestone 2", "Milestone 3"]

  projects.forEach(function(project) {
    console.log("-------------------------\n","Project: ", project)
    console.log("-------------------------")
    milestones.forEach(function(milestone) {
      console.log("\tMilestone: ", milestone)
      console.log("\tAssigned: ", projectAssigned(project, milestone))
      console.log("\tCompleted: ", projectCompleted(project, milestone))
      books.forEach(function(book) {
        console.log("\t\tBook: ", book)
        console.log("\t\tAssigned:", assigned(project, book, milestone))
        console.log("\t\tCompleted:", completed(project, book, milestone))
      })
    })
  })
}

status()
// OUTPUT:
// -------------------------
//  Project:  Hindi-ULB
// -------------------------
// 	Milestone:  Milestone 1
// 	Assigned:  0.024390243902439025
// 	Completed:  0.017661900756938603
// 		Book:  Matthew
// 		Assigned: 0.4642857142857143
// 		Completed: 0.17857142857142858
// 		Book:  Mark
// 		Assigned: 1
// 		Completed: 1
// 	Milestone:  Milestone 2
// 	Assigned:  0.012615643397813289
// 	Completed:  0.009251471825063078
// 		Book:  Matthew
// 		Assigned: 0.17857142857142858
// 		Completed: 0.07142857142857142
// 		Book:  Mark
// 		Assigned: 0.625
// 		Completed: 0.5625
// 	Milestone:  Milestone 3
// 	Assigned:  0.007569386038687973
// 	Completed:  0.004205214465937763
// 		Book:  Matthew
// 		Assigned: 0.10714285714285714
// 		Completed: 0.03571428571428571
// 		Book:  Mark
// 		Assigned: 0.375
// 		Completed: 0.25

I've worked the data and functions to change the nesting of project/milestone/book to project/book/milestone and have found no advantages one way or another, I could see either making sense for the data structure. It's easy to swap them out if needed.