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should point out there is also a difference between crawled, indexed and ranked.... though the later two are closely related. crawling is "hey look a new page" or "oh new content great" and it's then saved within google, this is then indexed - looking at what the content is about and it's relevance - then ranking comes along which is comparing.
in terms of categories, they are more reference points than definite areas, that is why you can actually input anything you want into there. so yes taxi is a go-er
the difference between the two is that one dictates you saying "we serve within 5 miles radius" it includes every city and town in that area... the second says we only serve this town or city ... (state country etc). the radius is more for local businesses and locations for companies who have multiple offices or shops.
it would be hard to do without knowing the system really well, though that plugin maybe able to help. The reason is that if those codes change they could mean any category - the last bit is likely not an issue of product name as url, but the category bit isn't so easy - unless it can be ignored and pulled from the CMS - again not being a magento expert I don't know how this would be done. sorry.
oh erm sounds a little odd set up - maybe worth trying http://shop.ecomdev.org/url-rewrite-indexer.html
I think that as your sitemap reflect your new urls and this is what the index is based on you are likely to have more indexed from what you say. I would suggest going to "indexed status" under health of GWT and click total index and ever crawled, this may help clear this up.
ok this needs clarifying
so your old urls want to be of the format /default/category/bags.html yes?
does the category relate to the 6 digit number in some way?
Are you using a shopping care of some kind or is this a bespoke system?
dealing with your indexing issue first - depending on when you submitted depends how soon those pages may be indexed. I say "may" because a sitemap (yes answering another question) is just an indicator of "i have these pages" it does not mean they will be indexed - indeed unless you've a small website you will never have 100% indexation in my experience.
Spiders (search robots) index / visit a website / page via another link. They follow links to a page from around the web, or the site itself. The more links from around the web the quicker you will get indexed. (this explains why if you've 10,000 pages you won't ever get a link from other websites to them all and so they won't all get indexed). This means if you've a web page that gets a ton of links it will be indexed sooner than those with just 1 link - assuming all links are equal (which they aren't).
Spiders are not cyclic in their searching, it's very ad-hoc based on links in your site and other sites linking to you. A spider won't be sent to spider every page on your site - it will do a small amount at a time, this is likely why 44 pages are indexed and not more at this point.
A sitemap is (as i say) an indicator of pages in your site, the importance of them and when they were updated / created. it's not really a definitive structure - it's more of a reference guide. Think of it as you being the guide on a bus tour of a city, the search engine is your passenger you are pointing out places of interest and every so often it will see something it wan't to see and get off to look, but it may take many trips to get off at every stop.
Finally, Canonicals are a great way to clear up duplicate content issues. They aren't 100% successful but they do help - especially if you are using dynamic urls (such as paginating category pages).
hope that helps
Having multiple pages targeting the same keywords is not a problem, its quite common. For instance if you have a e-commerce website dealing in fashion clothing for ladies, lots of your pages will target "fashion clothing" or "womens clothing" - thats a little different though to what I think you mean of ... I just want to target "keywords" to two pages and not others - is that right?
If that's correct then as long as both pages naturally lean towards those keywords and phrases you are fine. As with any SEO work don't force the story, don't include the keyword 25 times just because you can - it's not natural.
Hope that helps
I could be barking up the wrong tree. There is a difference between the price you say and the meta price which has two trailing 00's - this could be why it is ignored?
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.
pointing a folder would involve some DNS changes (to the CNAME record) - i think.
You would be best asking BC - it would be a similar process to pointing a subdomain to BC.
If you host a solution you are not always stuck in time, for example I use things like WooCommerce which is always being updated with new features and gives you great controls.
And just to clarify I am not saying that you cannot do the things YOU may want to do, but there are things that unless you've controls within the server you can't do - like implement GZIP for instance which can be a big deal on big sites.
moving the info site to BC is ok in general.
The reason both EGOL and I recommend having them together and on your own server is that you can control everything (see EGOL's list) and you aren't second guessing the settings on another server which you have no control over. It also means that things like templates can be made much more flexible to meet your exact needs and not just a few of your requirements.
If you can't some how point BC to a folder on your site then moving everything to BC is ok - the other option of course is to set up a new domain and let it exist in it's own right but you wouldn't get any benefit from that just as you wouldn't from a subdomain.
remove it temporarily and see if it fixes the issue? many an affiliate site have been caught loading malware on to devices by this kind of means - be careful
if you find the problem goes away great, contact the affiliate partner and ask them what is going on and to fix the problem - you won't be the only one in this boat i'm sure
you don't want GWT to show it 
you want to catch it first
find the offending code and delete it, its from an advert or affiliate site of some kind - could be a plugin sneaking it in - it's happened to me before on WP sites a plugin updates and brings bad code with it.
as much as they claim to ignore things like in within actually search they don't in semantic search because it could be quite important.
I would suggest for now keeping an eye on it, thats assuming its only the one keyword/phrase dropping?
something I recall (though could be wrong) from the disavow frenzy is that it can take a long time for those pages to be discounted - mainly is they only get picked up the next time a page is indexed I think. Hope that helps
can you post a link so we can see what exactly you are meaning - or post an example of the offending tag
not necessarily, overall good rank factors would mean that semantically you end up in the same place - you maybe the best at your term but they are best at relating to that term (if that makes sense)
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.