Anything else that compiles to javascript

Javascript

I would recommend lua. It's a minimalist scripting language so it's easy to grasp and also really fast (compared to other scripting languages like python). It's the first language I learned; I learned it because a game I played let you mod the client with lua scripts. It's not as useful as a language like Java, but a good amount of games have modding systems that use lua and you can embed it really easily in more advanced languages like C.

Edit: If you want some theory about programming languages you can check out some introductory computer science lectures from MIT, like Structure and Interpretation of Computer Programs

Apparently you're right. However, these changes only crop up when you're writing compilers or operating systems.

The instruction set is specified in the specification for each architecture so all computers in the same architecture will have the same instruction set. This is why a single binary will work for both AMD and Intel computers.

The x86 assembly wikibook walks you through basic assembly.

All x86 computers have the same number of registers. It'd be better to emulate hardware instead of buying it anyways.

Make an OS. There's tons of different things you can do in it and it's really easy to get a super barebones one up and running. The osdev wiki makes it really easy to start.

EDIT: The link is wiki.osdev.org

Have you heard of gitlab? It's basically an open source clone of github so you can host it yourself and actually have a good web interface.