By OP's own admission, the documentation coming with BINedit is rather meagre - it certainly tells you all you need to know to use the program, but at the same time it's hardly a suitable place to start for a new user.
I put this site together in an effort to alleviate problems such as these, and that includes writing some all-new BINedit tutorials! Choose from one of three links below to get started. In addition, I will also post links to any existing BINedit tutorials (at the moment, Phineus' tutorial on the MTMG is the only other tutorial out there).
For a very good tutorial on using BINedit to build track props, visit Phineus' BINedit Manual.
BINedit was developed mostly for use with MTM (1 and 2), and to my knowledge it is only with MTM2 that BINedit still receives the most widespread use. Phineus' BINedit Manual focuses on the basics which is usually more suited to track props but still provides the fundamentals for all modeling. Accordingly, my tutorials will have a narrow focus, mainly on using BINedit for building detailed MTM2 trucks. However, a lot of what is said here (and anywhere else) will be applicable to using BINedit for editing other TRI games, too.
1. Getting to know BINedit
This tutorial aims at introducing the program's features and functions. It describes the menu and keyboard commands and explains the program's interface. It will not teach you how to use BINedit, but it will explain what the program can do and also serves as a handy reference of the program's commands and functions.
2. Basic Tutorial - Putting it to work
This tutorial builds on the first by putting some of the previously described functions to practical use in building a simple model, and importing other models etc. It is aimed at the beginning to intermediate user. It has a version of OP's "Haystack Pyramid" mini-tutorial , followed by the making of a simple custom MTM2 truck.
3. Advanced Tutorial - MTM2 truck project
Drivey bites off way more than he can chew by trying to build a highly-detailed truck model entirely from scratch - and document the construction of it every step of the way (I hereby promise, in writing, never to be this stupid again). Find out what happens here.
FAQ, Tips and Tricks
This page will provide a quick reference for some Frequently Asked Questions, handy tips and tricks and general information on using BINedit effectively.