I recently worked on a project which required a updated version of the jQuery library. While there is the jQuery Update module, it only allows you to upgrade Drupal 6 to jQuery 1.3. If you really know what you're doing and want to upgrade beyond that version, you can either hack core or create your own simple module to do it. While hacking core is certainly the easier approach (simply overwriting misc/jquery.js with a newer version), it is very bad practice.
You say you want to build a website? It must be feature rich, flexible, extensible, powerful, and very web2.0. This is an important site, and you don't want to be locked in to someone else's framework, so you have decided the smartest approach is DIY. You have a small team of very experienced LAMP developers who have track record building successful sites. They've promised to meet your every requirement.
I've been putting it off for a few years, but I finally decided to upgrade devbee.com to Drupal 6.
I didn't really need to, but it bothered me that I wasn't running supported code and I figured I might learn something. And I did. Mostly obvious things that I should be familiar with already.
I've only ever played around with this. I don't like learning new things unless they are going to be truly useful to me. Drush is definitely something I shouldn't have ignored for so long. It comes in particularly handy when doing a site upgrade as you can download and install modules, clear cache, set variables, run DB updates and a lot more all from the command line. This tool is crazy good if you're comfortable in a terminal.
The following is a guest post by Mitchel Xavier
One of the challenges of developing with Drupal is to understand Drupal’s structure. Until now, when working with the DOM structure, the DOM inspector has been the best tool for viewing the structure. A new tool has been created to make the visualization of the DOM structure much easier to interpret. It is a Firefox add-on and is called Tilt 3D. It creates 3 dimensional interactive representation of the DOM elements as a layered visual image.
I just found this very cool screencast creation tool that is free. It's called Jing. Installation is quick and pretty easy (though it does require the .NET 3.0 libraries for the Windows version).
Here's a sample screencast, a quick demo of cscope as a development tool.