A no-follow, in terms of juice, would actually hurt your goals as the link still gets allocated the juice portion but it doesn't flow through.  **Each no-follow link will siphon off a little juice. **

See http://support.google.com/webmasters/bin/answer.py?hl=en&answer=96569

The effects of navigational links are diminished somewhat as Google treats them differently compared to content links.  To help solidify this, surround the footer with

<nav></nav>

tags.

Review: http://www.seomoz.org/blog/10-illustrations-on-search-engines-valuation-of-links #5

Generally, remove any site wide links that aren't always needed and place them on page where users would like the details.  For instance, use a search form instead of a link to the search page.

Fact is, the robots file alone will never work (the link has a good explanation why - short form: all it does is stop the bots from indexing again).

Best to request removal then wait a few days.

Sounds like (from other discussions) you may be stuck requiring a dynamic robot.txt file which detects what domain the bot is on and changes the content accordingly.  This means the server has to run all .txt file as (I presume) PHP.

Or, you could conditionally rewrite the /robot.txt URL to a new file according to sub-domain

RewriteEngine on
RewriteCond %{HTTP_HOST} ^subdomain.website.com$
RewriteRule ^robotx.txt$ robots-subdomain.txt

Then add:

User-agent: *
Disallow: /

to the robots-subdomain.txt file

(untested)

Option 1 could come with a small performance hit if you have a lot of txt files being used on the server.

There shouldn't be any negative side effects to option 2 if the rewrite is clean (IE not accidently a redirect) and the content of the two files are robots compliant.

Good luck

You should do a remove request in Google Webmaster Tools.  You have to first verify the sub-domain then request the removal.

See this post on why the robots file alone won't work...

http://www.seomoz.org/blog/robot-access-indexation-restriction-techniques-avoiding-conflicts

The fact a Caps create a 404 error on LAMP site is a pet peeve of mine - so is the fact Google thinks mix cases on IIS are separate (thus duplicate) URLs.

Too arbitrary to be picky about and cause user frustration.

Thanks goodness at lease DoMaInS can be what ever.

Before you delete anything, submit a ticket to the help desk.  They may be able to fix it up or point to why it's happening.

http://www.seomoz.org/help