Running sub directory multisite from a subfolder

This is my first question. I am a fair PHP developer, and have followed the instructions on the codex but something isn't working and I don't know why.

I want to run a wordpress multisite on a domain from a subdirectory. So, the urls will be
http://www.dmgstories.com/site1
http://www.dmgstories.com/site2
http://www.dmgstories.com/site3
etc...

That is simple enough. However, I want the files to live in at dmgstories.com/wp(/wp-admin, wp-includes,etc).

I first installed Wordpress in /wp/ and then followed the instructions to run it from top-level. Worked fine. I then enabled Multisite. The admin area gave me some problems because it was leaving off the /wp/ prefix in some of the forms, but I hacked network_admin_url() to fix that problem.

The top level blog works fine (www.dmgstories.com) which it shouldn't. When I try one of the sub-directory sites, I get text (not the right text) but no styling whatsoever.

I have searched for forum posts or lessons. Nada. I feel like this should be a simple thing, but I can't find what I need. There is no content, so I am willing to re install.

Any thoughts?

Thank you!

PS: I'd also like to move the wp-content and plugins folders. I saw how to do that, but didn't want to until I got this working.