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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.

What's the maximum amount of html pages that one should put in a folder, to get the best SEO GoggleBot crawl?  I'm aware that there's a limit of 10,000 on most servers, but was curious to know if a lesser amount of pages would be better, for crawling and indexing purposes.  Also curious on peoples opinions on whether .jpg and .gif files should follow similiar rules.

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.

Do I disavow the entire domain, or just the url where the link exists?

I've been noticing a growing amount of spammy directories using my title Meta-Tag to create a link back to my site.  Since my title uses competitive keywords, these external links on spammy directories look over optimized and I fear an algo penalty might get triggered.  Should I be concerned and what can I do?

Looks like Google doesn't trust your site enough to offer the pages you think are logical as results for the query.  I'd say G Bot isn't confident about your content, and is triggering an algo filter.  True, internal links may be causing the confusion, but I'd also suggest checking your external link profile to make sure relevant sites are leading G Bot back to your blog.

Sounds like you've got a php site that's dynamically creating pages.  You have to find the person who wrote the script and have them edit the template to add a canonical tag that inserts the correct url when the page is generated.  Your not going to be able to insert a static canonical tag.

I do think NoFollow is more pertinent for external sites linking to your site, and not so much inner site links used for navigation.  I'd be more concerned with the amount of keywords used in the metatags.

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.

Client is thinking of adding a directory to an eCommerce site which users would find useful.  It would help users find other services and vendors that are specific to the niche of products this site is selling.  My only concern is it would create a number of external links to other sites.  Even though they're related, would this diminish our standing with Google search?

I will give GSiteCrawler a shot.  I've been very impressed with the free ScreamFrog crawler, and if I were to select an alternative today, it be this.  Just debating with myself the cost for the paid version.

It's html with embedded cgi-bin eCommerce software that produces dynamic pages.

The trouble xml-sitemaps seems to have is with rich snippets and structured data. It seems to have trouble getting it to recognize pages with that code.  I was wondering if anybody else has had a similar problem?  Sites that I have without snippets, work fine.

I was wondering if everyone could recommend what XML Sitemap generators they use.  I've been using XML-Sitemap, and it's been a little hit and miss for me.  Some sites it works great, other it really has serious problems indexing pages.  I've also uses Google's, but unfortunately it's not very flexible to use.

Any recommendation would be much appreciated.

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!

The 301 from the old domain is going to carry good and bad juice over to your new URL, consequently I think your doing the logical thing by trying to eliminate as many of the bad links as possible.  If you remove, the 301's, you'd be starting from scratch.  Since you've initiated 301's I'd hold your course, and start building new links to the current url.

The Google+ Page that appears under local listings in Google for a company I work for, was setup by an advertiser, such as Yellow Pages.  I'm not sure how they got control of it, but apparently somebody at this agency set it up, and verified the url.  The G+ page is now outdated, and needs to be updated.  More importantly, I have to manage the page, and not this third party.   I sent a request to Google to transfer ownership.

My question is, has anybody had any luck in getting control of a Google+ page which was setup by the wrong party, back?  As a backup, I've initiated a plan of creating a new Google+ page with the account info from the WMT's account of the url.  I figure, that might have more authority than a page erroneously setup by a third party.  My hope is it would eventually replace the Google+ page the currently shows in local returns.  Any thoughts or comment would be appreciated.

I'm tracking keyword results in Rank Tracker, but I can't confirm the positions when I do a Google search for the tracked keywords.  Does anybody know why RT says the site should be #23, but is not actually in Google?

Is there a way to check Google results from different data centers?  If I recall, Google allowed the option to view results from different cities, though I don't know if they still allow this.

Sounds similar to paginate issues, and the potential to create duplicate content in the eye's of google, particularly if you're using a template.  Not a serious issue if this occurs for 1 or 2 clicks, but if viewer are going to do this for 5 or more times after the initial landing page, it might be a problem with the meta-tags.

It's my experience Google indexes everything on your site, over time.  Logic is to place most important pages in the upper tiers because googlebot won't get everything at once.