Hi, there,
The reason that putting html in the htdocs directory is that the HTTP Server is serving your home pages instead of the Portal Server serving them through HTTP. You won't find the directory wps/portal anywhere on your hard drive because it is a base URI configuration that is set during the install and it's virtual. If you just let it default, then WPS sets it up for you in the directory that you've been trying to find, so I don't think that's the root of your problem.
This is a really difficult product to install. To make it run successfully on my machine, I had to install it, uninstall it, reinstall Windows 2000 and start from scratch.

Hopefully this won't be the case with you.
A few suggestions:
If you didn't use the default id and password (wpsadmin), go back and reinstall using these.
Make sure that DB2 has the correct fixpack installed and that you can connect to the WPS40 DB.
If you're using Single Server Edition of WAS, make sure that you start the server with the correct configuration file (portal-cfg.xml I think).
Regenerate the WebSphere plugin in WAS on the node associated with your host.
Most of the install went through, I'm guessing from your post, so if you haven't read the 'Troubleshooting' Section in the InfoCenter, it might behoove you to do so to see if you've missed anything (although this section is about 10 times too short!)