its not that complicated, copy the new /concrete directory over the old on then go tohttp://site.com/tools/required/upgrade...

I totally agree, it should be easy. But since no such directory called "required" exists under "tools" it is impossible to accomplish.

its actually in <root>/concrete/tools/required/upgrade.php

go to
site.com/index.php/tools/required/upgrade

The upgrade page is not an actual directory, it is a virtual path, aka a path rewrite. The path site.com/tools/required/upgrade is really site.com/index.php/tools/required/upgrade.

Try that and let us know what happens.

I'm also having issues with the upgrade to 5.4.0.5.

I followed the instructions, site came up fine, dashboard came up fine, however, when trying to access the marketplace, I get this error:

Warning: require_once(/home1/user/public_html/root/concrete/config/../helpers/concrete/marketplace/blocks.php) [function.require-once]: failed to open stream: No such file or directory in /home1/user/public_html/root/concrete/libraries/loader.php on line 220

Fatal error: require_once() [function.require]: Failed opening required '/home1/user/public_html/root/concrete/config/../helpers/concrete/marketplace/blocks.php' (include_path='.:/usr/lib64/php:/usr/lib/php:/home1/user/public_html/root/libraries/3rdparty:/home1/user/public_html/root/concrete/config/../libraries/3rdparty') in /home1/user/public_html/root/concrete/libraries/loader.php on line 220

Why do you have to rebuild from scratch? Didn't you back up your database and web root?
Anyway, maybe you shouldn't use the pretty URLs for upgrade and just loadhttp://www.yoursite.com/index.php/tools/required/upgrade... (Note: if this does not work, tryhttp://www.yoursite.com/index.php/tools/required/upgrade.php)...
It's all in here:http://www.concrete5.org/documentation/installation/upgrading_concr...

This is the third website that I've attempted to upgrade and none of them work. I've tried every variation of upgrade or upgrade.php script and all I get is a blank white page or a 404 error.

There is no /required folder. There is a /concrete/tools/upgrade.php file but doesn't do anything when it's called.

Before upgrading try to disable Pretty URLs from your Dashboard > Sitewide Settings and also disable cache and clear the cache.
After that run yoursite.com/index.php/tools/upgrade.php
See if that works

George

instead of trying to open the screen which should allow you to confirm it you can try to force it by using this:

www.www.yoursite.com/tools/upgrade?force=1... orwww.www.yoursite.com/index.php/tools/upgrade?force=1...

This takes away the need for a confirmation and forced the upgraded to be completed.