If you are really interested in learning low level stuff, I would recommend taking a formal course in in Electrical/Computer Engineering discipline at a University in following subjects or get a text book and go through it yourself:

Logic Design and Switching Theory (e.g. Friedman)

Computer Architecture and Organization (e.g. by William Stallings)

The kind of programming you are referring to, is probably only used in VHDL/Verilog etc. You will also need very very strong mathematical background to get a good grasp of the concepts. This however, may not be helpful for computer science apps, not even in designing an operating system as I believe the most operating Systems were written in C or Assembly and not Register/Hardware Level. The assembly/C language program, once compiled is usually mapped to the Instruction Set thats provided by the vendor of the hardware. Designing an OS using such an instruction set alone would be as if you are trying to kill an elephant with a slingshot.

Happy Coding!!