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Thanks for all the input.  Google does seem to crawl everything these days, so I'm also in conclusion if the files fit, they'll get crawled.  Sitemaps, internal links and optimized images are all a must.

Disavowing the entire domain seems like the safest thing to do, because there may be other links that haven't caught my attention yet.  If Google doesn't require the exact location, then I think this is what I will do.

Thanks for the input SamuelScott.  Generally, I plan to keep the external links well under 100 per page, by breaking them into sub-categories.  I agree with your assessment that if it's good for the viewer, then it's good with Google because all they're suggestions on site design is geared towards the end user. My main concern, as you've stated, is that by leading users off the site, would I not reduce the page rank, and ultimately ranking.  I appreciate that you seem to think, not.

I would give DYNO Mapper a try. It's great Sitemap Generator that includes link / inventory information, Google Analytics integration, and comments for collaboration. It can import xml or scan urls pretty accurately. It is probably more useful for planning architecture than exporting for Google,

Yup, that's where I'm at right now.  Got an email reply from G stating to wait up to 7 days for whoever has control to contact us.   At that point, I'll contact G directly.  Thanks!

Hey alrockn, The search engines - Google, Yahoo! & Bing - all maintain multiple indices that run across multiple datacenters. This means if you query different datacenters, you can get somewhat different ranking results. As others have mentioned, other elements, such as personalization, geography and search history (even if you're logged out of your Google/search engine account) can also influence ranking positions. Hence, there can be a lot of variation in what different people, searching from different computers/locations might see in the rankings. Our solution has been to run searches from a variety of IP addresses and IP blocks using non-personalized, search history/location agnostic requests. In our experience, these have provided the most accurate results, showing what the "most" users see, though we know there's still quite a bit of room for fluctuation. If you have suggestions about how we might improve the technical process of fetching rankings data to get better data, please let us know and we'll pass it on to our engineering team. We're always looking for ways to get you better data

May concern was these screwed up links would somehow impair ranking, but I guess not.  Thanks for the link.

Exactly, I removed some URLS, and tweeked the priorities, in Dreamweaver, then saved.  I want to make sure nothing got messed up.   WMT has the ability to test before submitting, which I just learned.  I used xml-sitemaps.com stand alone, which passed the WMT test.  Now I'm going to do some editing, and try it again before submitting.

Thanks guys! Upon further research what's happening is "Entity Escaping", where symbols have to use a code...ie & = &, so it's all good. http://www.sitemaps.org/protocol.html

If there is no relevant new location to 301 to and you are dealing with way too many files to individually 301 them, then you can simply delete them so Google will encounter the 404 error page and remove those files from the index. That being said, if there are any old files that actually rank for search queries and generate organic traffic to your site, then I would recommend at least 301'ing those if possible so you don't lose the traffic as a result of the page being removed altogether.

PDG-Commerce

A 401 is 'unauthorized' - is that the code it would produce, or a different error (or a typo!)? That could work in theory - I'd be a bit hesitant about the extra step involved in 301ing to get to an error page on a different site. In general, the fewer steps you make Google go through, the better. This method would mean that your new site should not be "credited" with the bad links, however.

Closing this particular thread as it's a duplicate - answers going up on the other thread.