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Myself, I usually create another email address that doesn't mention the client nor the agency. From there I send my pitch for the link saying I represent a client that is in the X business and would like to link through high quality content on the target site.
From that respect, if you are putting in an Author Bio you could use a premade bio or your own bio that again doesn't have to mention client or agency.
If they haven't affected you this far, i'd say just leave them alone, they don't seem to be doing any harm.
hide it using a robots.txt file - though you could also use the noindex meta tag ... this being said search engines in general recognize sitemap pages and aren't too fussed by them, its a good jumping off point for them to find info.
The first thing that springs to mind is your robots.txt file. Is robots.txt blocking something it shouldnt be? it sounds like it might be if Google literally can't get onto your site to crawl it.
When was the last time your individual URLs were indexed?
completely agree. also a domain doesn't mean its your companies name, in many cases it can be but not always. good luck.
It's dependant on what the directory is. Yes Google doesn't like paid links, but some customers may still use online directories so from that aspect they are good. Look at a directory and see whether they are ones your customers will use.
As William Lau said, Directories, for ranking, don't work as well as they used to anymore.
if many show 1 url as duplicate this could be due to non-ww and www redirect issues or be related to dynamic urls (common for paginated pages)
if these are the case fix the redirect issue to either non-www or www and fit in a canonical tag to paginated pages. (google is your friend for finding code)
The thing to remember is that the HTML version should only ever be used for users and not to redirect robots if they hit a 404 on your .xml file. The reason for this is that search engines may still see the file as 404 after the redirect or a 301 redirect, if the later you then have an issue of search engines thinking it was there but is now the html page. Which of course is not a good thing.
I would advise ensuring the fall back never happens to robots / spiders - if the file is just a 404 SE's will return to it, they may not if it is 301 redirect.
Also something to consider is that you don't need to re-submit the sitemap ever whilst your sitemap is in the same location and has the same title it always did. Google will on a regular basis fetch that sitemap without resubmitting.
I would say update the sitemap if you've a new page or deleted it - but its not a huge issue really if you are out by a day or 14 - unless your site is very busy with lots of visitors it's not that important to google, also I find they prefer natural crawling and finding than being told there is one new page - this said a whole section change is definitely worth updating it.
Congratulations 
I've really started getting into the community and helping others too and it is very gratifying and also helps broaden my own SEO expertise as well as coming across new people in the community.
Congratulations on your top 100 and I hope to get there at some point myself too
There was a good discussion on this very topic a week or so ago. You can find it here:
http://www.seomoz.org/q/is-widgetbait-no-longer-valid-at-all-according-to-the-new-quality-guidelines
Few things... make sure you have a sitemap that is always upto date and submitted to search engines - this will encourage them to view your content first and recognise it as belonging to your domain.
In addition to this put links in your content to other parts of your site, if it gets scraped it will probably be with the links in it and so anyone actually wanting real content can get through.
If there are thousands from the same domain coming to your site, disavow the base url and also report that url for spam (it's your copyright). In fact if you notice a small site scraping you, do that after you've tried to contact them.
If this still doesn't stop them look at your logs and see where their crawlers are coming from and block their IP's.
On one of my old site I blocked the whole of China at one point because it was constantly being barraged by scrapers and people trying to guess account passwords.
Hope that helps
I would suggest "flower pots- plastic flower pots with free delivery" ... reasons same as above, though I would suggest possibly using "plastic flower pots with free delivery | brand" to remove the repetition which can often be seen as spamming and keyword stuff especially as you are then likely to use the term again in your meta description and url
the url SEOMoz is crawling is the page SE's will see - anything after #! or even just # will be ignored - it's a reference for point of scripts and not search engines. by default anyway.
There are ways around this to some extent, though not totally.
I won't bore you with great detail here or give you examples of how to, instead I shall leave that to Google Developers pages.
If they have access to the domains they will, if they are that kind of company, delete them. If they are on blogs where they have outreached to webmasters etc.. I think they will probably leave them be, as it would be a lot of work to get rid.
Another big problem, which some 'snake oil' SEO's use is to build links to a URL that redirects to your site. That means if you cancel, they just remove the redirect and you lose all your links.
By the sounds of it they have done outreach and i'd be leaning more to say you would probably be safe if you cancelled, but again I wouldn't be 100% certain without being able to have a look.
Have a chat with your SEO consultant and maybe just ask how they build their links.
two limits to be aware of here
There is no need to link in html to your sitemap if you are submitting it by webmaster tools, though a poke can be helpful from robots.txt which would look something like :
Sitemap: http://www.example.com/sitemap.xml
and go under your various statements (should be the last thing)
Hope this helps
this sounds like a bug more than anything to me - maybe the moz team can shed some light on this.
The only time I've found a difference in ranking for caps vs non -caps is due to semantics and google knowing things like "church" and "Church" are different entities - in your own example though this wouldn't be the case ... hence i think its a bug.
mmm a puzzle
14 including spaces 
Joke, use it naturally, the same in your title and content -do not force keywords into your content or descriptions, Google knows when it's being manipulated and over the past few years has cracked down on keyword spammers hugely.
Just to add a discussion into here.
People say paying for the link is against Google guidelines etc... But how does Google know the difference between a paid and unpaid link? they both look the same in the eyes of Google surely?
How can an algorithm know if you've sent some money to someone over Paypal for example? Surely its only differentiating between poor links and good quality links?