http://www.amazon.com/Computer-Systems-Programmers-Perspecti...
https://blogs.oracle.com/ksplice/entry/hello_from_a_libc_fre...
http://www.muppetlabs.com/~breadbox/software/tiny/teensy.htm...
http://timelessname.com/elfbin/
A wee bit heavy, but it's comprehensive. It deals with what happens when you run code, how the architecture of the computer works (by and large) including at the logic level:
http://www.amazon.co.uk/Computer-Systems-Programmers-Randal-...
If you want to go lower (and higher).. look at Understanding the Linux kernel for a good understanding of how an OS is put together, with specific examples i.e. Linux.
Code, by Petzold, deals with logic and computers from the ground up. It starts with relays and builds them up into gates and usable arithmetic blocks.
http://www.amazon.co.uk/Code-Language-Computer-Hardware-Soft...
http://www.amazon.co.uk/Understanding-Linux-Kernel-Daniel-Bo...
The physics is fairly simple, at least from a CRT or LED display perspective. Gets more tricky dealing with interconnecting microprocessors because a good chunk is vendor specific.
I think this kind of project is well suited to a guide on how to build a computer from the ground up, starting with logic gates, writing a real time OS and developing a scripting language that will run and compile on it. Then you can skip a lot of largely extraneous stuff and have a solid understanding of how the hardware works.
A great book to learn more: http://www.amazon.com/Computer-Systems-Programmers-Perspecti...
[1] http://tams-www.informatik.uni-hamburg.de/applets/hades/webd...
In no particular order:
1- http://www.amazon.com/C-Programming-Language-2nd-Edition/dp/...
2- http://www.amazon.com/The-Answer-Book-Solutions-Programming/...
3- http://www.amazon.com/The-Standard-Library-P-J-Plauger/dp/01...
4- http://www.amazon.com/C-Traps-Pitfalls-Andrew-Koenig/dp/0201...
5- http://www.amazon.com/Expert-Programming-Peter-van-Linden/dp...
6- http://www.amazon.com/Data-Structures-In-Noel-Kalicharan/dp/...
7- http://www.amazon.com/Data-Structures-Using-Aaron-Tenenbaum/...
8- http://www.amazon.com/Mastering-Algorithms-C-Kyle-Loudon/dp/...
9- http://www.amazon.com/Code-Complete-Practical-Handbook-Const...
10- http://www.amazon.com/Design-Patterns-Elements-Reusable-Obje...
11- http://www.amazon.com/The-Mythical-Man-Month-Engineering-Ann...
12- http://www.amazon.com/The-Programming-Language-4th-Edition/d...
13- http://www.amazon.com/The-Standard-Library-Tutorial-Referenc...
14- http://www.amazon.com/API-Design-C-Martin-Reddy/dp/012385003...
15- http://www.amazon.com/The-Linux-Programming-Interface-Handbo...
16- http://www.amazon.com/Computer-Systems-Programmers-Perspecti...
17- http://www.amazon.com/System-Programming-Unix-Adam-Hoover/dp...
18- http://www.amazon.com/Memory-Programming-Concept-Frantisek-F...
19- http://www.amazon.com/Memory-Management-Implementations-Prog...
20- http://www.amazon.com/UNIX-Filesystems-Evolution-Design-Impl...
21- http://www.amazon.com/PCI-System-Architecture-4th-Edition/dp...
22- http://www.amazon.com/Universal-Serial-System-Architecture-E...
23- http://www.amazon.com/Introduction-PCI-Express-Hardware-Deve...
24- http://www.amazon.com/Serial-Storage-Architecture-Applicatio...
25- http://www.amazon.com/SATA-Storage-Technology-Serial-ATA/dp/...
26- http://www.amazon.com/Beyond-BIOS-Developing-Extensible-Inte...
27- http://www.amazon.com/Professional-Assembly-Language-Program...
28- http://www.amazon.com/Linux-Kernel-Development-3rd-Edition/d...
29- http://www.amazon.com/Version-Control-Git-collaborative-deve...
30- http://www.amazon.com/Embedded-Software-Primer-David-Simon/d...
31- http://www.amazon.com/Programming-Embedded-Systems-C/dp/1565...
32- http://www.amazon.com/Making-Embedded-Systems-Patterns-Softw...
33- http://www.amazon.com/Operating-System-Concepts-Abraham-Silb...
34- http://www.amazon.com/Performance-Preemptive-Multitasking-Mi...
35- http://www.amazon.com/Design-Operating-System-Prentice-Hall-...
36- http://www.amazon.com/Unix-Network-Programming-Sockets-Netwo...
37- http://www.amazon.com/TCP-Illustrated-Volume-Addison-Wesley-...
38- http://www.amazon.com/TCP-IP-Illustrated-Vol-Implementation/...
39- http://www.amazon.com/TCP-Illustrated-Vol-Transactions-Proto...
40- http://www.amazon.com/User-Interface-Design-Programmers-Spol...
41- http://www.amazon.com/Designing-Interfaces-Jenifer-Tidwell/d...
42- http://www.amazon.com/Designing-Interfaces-Jenifer-Tidwell/d...
43- http://www.amazon.com/Programming-POSIX-Threads-David-Butenh...
44- http://www.intel.com/p/en_US/embedded/hwsw/software/hd-gma#d...
45- http://www.intel.com/content/www/us/en/processors/architectu...
46- http://www.intel.com/p/en_US/embedded/hwsw/hardware/core-b75...
47- http://www.hdmi.org/index.aspx
48- http://en.wikipedia.org/wiki/Digital_Visual_Interface
49- http://www.amazon.com/Essential-Device-Drivers-Sreekrishnan-...
50- http://www.amazon.com/Making-Embedded-Systems-Patterns-Softw...
51- http://www.amazon.com/Python-Programming-Introduction-Comput...
52- http://www.amazon.com/Practical-System-Design-Dominic-Giampa...
53- http://www.amazon.com/File-Systems-Structures-Thomas-Harbron...
54- ...well, I'll stop here.
Of course, the equivalent knowledge can be obtained by trial-and-error, which would take longer and might result in costly errors and imperfect design. The greater danger here is that a sole developer, without the feedback and interaction of even a small group of capable and experienced programmers could simply burn a lot of time repeating the mistakes made by those who have already trenched that territory.
If the goal is to write a small RTOS on a small but nicely-featured microcontroller, then the C books and the uC/OS book might be a good shove in the right direction. Things start getting complicated if you need to write such things as a full USB stack, PCIe subsystem, graphics drivers, etc.
Computer Systems: A Programmer's Perspective
http://www.amazon.com/dp/0136108040is superior to the widely mandated
Computer Architecture: A Quantitative Approach
for software engineers and programmers. The former has less hardcoded numbers than the latter and more timeless principles.
http://csapp.cs.cmu.edu/ http://www.amazon.com/Computer-Systems-Programmers-Perspecti...
This is a textbook out of Carnegie Mellon that I was exposed to in grad school. It goes into all kinds of details of processor architecture, memory, I/O, assembly programming, etc. while staying focused on its audience of a systems programmer in C. It's wonderful.
http://www.amazon.com/Computer-Systems-Programmers-Perspecti...
Also, to get better understanding of x86 ISA I followed the old i386 manual[2]. Its old but much more smaller. Perhaps once you feel comfortable, you can move to newer manuals. I never read newer ones (because I never actually needed assembly for any project, was just studying for fun).
[1] http://www.amazon.com/Computer-Systems-Programmers-Perspecti...
[2] http://css.csail.mit.edu/6.858/2015/readings/i386.pdf