I've posted this before but I'll repost it here:

Now in terms of the question that you ask in the title - this is what I recommend:

Job Interview Prep

1. Cracking the Coding Interview: 189 Programming Questions and Solutions
   
2. Programming Interviews Exposed: Coding Your Way Through the Interview
   
3. Introduction to Algorithms
   
4. The Algorithm Design Manual
   
5. Effective Java
   
6. Concurrent Programming in Java™: Design Principles and Pattern
   
7. Modern Operating Systems
   
8. Programming Pearls
   
9. Discrete Mathematics for Computer Scientists
   
   

   Junior Software Engineer Reading List
   

   
   

   Read This First
   

   
   

10. Pragmatic Thinking and Learning: Refactor Your Wetware
    
    

    Fundementals
    

    
    

11. Code Complete: A Practical Handbook of Software Construction
    
12. Software Estimation: Demystifying the Black Art
    
13. Software Engineering: A Practitioner's Approach
    
14. Refactoring: Improving the Design of Existing Code
    
15. Coder to Developer: Tools and Strategies for Delivering Your Software
    
16. Perfect Software: And Other Illusions about Testing
    
17. Getting Real: The Smarter, Faster, Easier Way to Build a Successful Web Application
    
    

    Understanding Professional Software Environments
    

    
    

18. Agile Software Development: The Cooperative Game
    
19. Software Project Survival Guide
    
20. The Best Software Writing I: Selected and Introduced by Joel Spolsky
    
21. Debugging the Development Process: Practical Strategies for Staying Focused, Hitting Ship Dates, and Building Solid Teams
    
22. Rapid Development: Taming Wild Software Schedules
    
23. Peopleware: Productive Projects and Teams
    
    

    Mentality
    

    
    

24. Slack: Getting Past Burnout, Busywork, and the Myth of Total Efficiency
    
25. Against Method
    
26. The Passionate Programmer: Creating a Remarkable Career in Software Development
    
    

    History
    

    
    

27. The Mythical Man-Month: Essays on Software Engineering
    
28. Computing Calamities: Lessons Learned from Products, Projects, and Companies That Failed
    
29. The Deadline: A Novel About Project Management
    
    

    Mid Level Software Engineer Reading List
    

    
    

    Read This First
    

    
    

30. Personal Development for Smart People: The Conscious Pursuit of Personal Growth
    
    

    Fundementals
    

    
    

31. The Clean Coder: A Code of Conduct for Professional Programmers
    
32. Clean Code: A Handbook of Agile Software Craftsmanship
    
33. Solid Code
    
34. Code Craft: The Practice of Writing Excellent Code
    
35. Software Craftsmanship: The New Imperative
    
36. Writing Solid Code
    
    

    Software Design
    

    
    

37. Head First Design Patterns: A Brain-Friendly Guide
    
38. Design Patterns: Elements of Reusable Object-Oriented Software
    
39. Domain-Driven Design: Tackling Complexity in the Heart of Software
    
40. Domain-Driven Design Distilled
    
41. Design Patterns Explained: A New Perspective on Object-Oriented Design
    
42. Design Patterns in C# - Even though this is specific to C# the pattern can be used in any OO language.
    
43. Refactoring to Patterns
    
    

    Software Engineering Skill Sets
    

    
    

44. Building Microservices: Designing Fine-Grained Systems
    
45. Software Factories: Assembling Applications with Patterns, Models, Frameworks, and Tools
    
46. NoEstimates: How To Measure Project Progress Without Estimating
    
47. Object-Oriented Software Construction
    
48. The Art of Software Testing
    
49. Release It!: Design and Deploy Production-Ready Software
    
50. Working Effectively with Legacy Code
    
51. Test Driven Development: By Example
    
    

    Databases
    

    
    

52. Database System Concepts
    
53. Database Management Systems
    
54. Foundation for Object / Relational Databases: The Third Manifesto
    
55. Refactoring Databases: Evolutionary Database Design
    
56. Data Access Patterns: Database Interactions in Object-Oriented Applications
    
    

    User Experience
    

    
    

57. Don't Make Me Think: A Common Sense Approach to Web Usability
    
58. The Design of Everyday Things
    
59. Programming Collective Intelligence: Building Smart Web 2.0 Applications
    
60. User Interface Design for Programmers
    
61. GUI Bloopers 2.0: Common User Interface Design Don'ts and Dos
    
    

    Mentality
    

    
    

62. The Productive Programmer
    
63. Extreme Programming Explained: Embrace Change
    
64. Coders at Work: Reflections on the Craft of Programming
    
65. Facts and Fallacies of Software Engineering
    
    

    History
    

    
    

66. Dreaming in Code: Two Dozen Programmers, Three Years, 4,732 Bugs, and One Quest for Transcendent Software
    
67. New Turning Omnibus: 66 Excursions in Computer Science
    
68. Hacker's Delight
    
69. The Alchemist
    
70. Masterminds of Programming: Conversations with the Creators of Major Programming Languages
    
71. The Information: A History, A Theory, A Flood
    
    

    Specialist Skills
    

    
    In spite of the fact that many of these won't apply to your specific job I still recommend reading them for the insight, they'll give you into programming language and technology design.
    
    

72. Peter Norton's Assembly Language Book for the IBM PC
    
73. Expert C Programming: Deep C Secrets
    
74. Enough Rope to Shoot Yourself in the Foot: Rules for C and C++ Programming
    
75. The C++ Programming Language
    
76. Effective C++: 55 Specific Ways to Improve Your Programs and Designs
    
77. More Effective C++: 35 New Ways to Improve Your Programs and Designs
    
78. More Effective C#: 50 Specific Ways to Improve Your C#
    
79. CLR via C#
    
80. Mr. Bunny's Big Cup o' Java
    
81. Thinking in Java
    
82. JUnit in Action
    
83. Functional Programming in Scala
    
84. The Art of Prolog: Advanced Programming Techniques
    
85. The Craft of Prolog
    
86. Programming Perl: Unmatched Power for Text Processing and Scripting
    
87. Dive into Python 3
    
88. why's (poignant) guide to Ruby

Books on project management, software development lifecycle, history of computing/programming, and other books on management/theory. It's hard to read about actual programming if you can't practice it.

Some of my favorites:

• Code: The Hidden Language of Computer Hardware and Software - GREAT choice I notice you already have listed. Possibly one of my favorite, and this should be on everyone's reading list who is involved in IT somehow. It basically how computers and programming evolved and gets you in a great way of thinking.
  
  
• The Code Book: The Science of Secrecy from Ancient Egypt to Quantum Cryptography - Another great history book on code and how things came to be. It's more about crypto, but realistically computing's history is deeply rooted into security and crypto and ways to pass hidden messages.
  
  
• Software Project Survival Guide - It's a project management book that specifically explains it in terms of software development.
  
  
• The Art of Intrusion: The Real Stories Behind the Exploits of Hackers, Intruders and Deceivers - A fun collection of short hacking stories compiled and narrated by Kevin Mitnick, one of the most infamous hackers. Actually, any of Mitnick's books are great. Theres a story in there about a guy who was in jail and learned to hack while in there and get all kind of special privileges with his skills.
  
  
• Beautiful Data: The Stories Behind Elegant Data Solutions - Most of the books in the "Beautiful" series are great and insightful. This is one of my more favorite ones.
  
  
• A Guide to the Project Management Body of Knowledge: PMBOK(R) Guide - THE guide to project management from the group that certifies PMP... boring, dry, and great to help you get to sleep. But if you're committed enough, reading it inside and out can help you get a grasp or project management and potentially line you up to get certified (if you can get the sponsors and some experience to sit for the test). This is one of the only real certifications worth a damn, and it actually can be very valuable.
  
  You can't exactly learn to program without doing, but hopefully these books will give you good ideas on the theories and management to give you the best understanding when you get out. They should give you an approach many here don't have to realize that programming is just a tool to get to the end, and you can really know before you even touch any code how to best organize things.
  
  IF you have access to a computer and the internet, look into taking courses on Udacity, Coursera, and EDX. Don't go to or pay for any for-profit technical school no matter how enticing their marketing may tell you you'll be a CEO out of their program.

I've ordered the book and will check it out.

Not sure what you mean by "where things started to go wrong". Are you saying Agile is a bad choice?