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Either should be fine from an SEO perspective. I'd decide based on what would make most sense to users - probably the second.

The visible PageRank is only updated about 4 times a year. How long have you been building links to your site?

Also, I notice you only have a very few backlinks to your site - you may not have enough to get PR1 yet.

Yes, it sounds like Google has indexed both copies, so that would be duplicate content.

302 redirects mean the page has temporarily moved. It sounds like the pages are only temporary, so that would be the correct thing to use. You could also use nofollow or canonical tags, too.

A nofollow won't stop the page from getting indexed if it is linked to from elsewhere on the web.

Thorsten,

That's a bit tough to answer quickly, because there are so many things that could negatively affect the trust or authority of a website. A few include:

Other websites the page/site links to

Usage or gray or black hat tactics

Quality of content on the site

Overall quality of the site

Authority of the linking page

Most or all of those links will be nofollow. They may still be helpful, but I would suggest focusing on other strategies to build dofollow links.

1. 9932 orphan files - does just removing them affect my SEO.. I like a clean house, can I somehow use them to my benefit?

If they are truly orphaned (not used by anyone or linked to from anywhere), you could probably just delete them.

2. Hundreds of 404s with many external "follow" links that we are no longer getting juice from

I would probably 301 redirect them to a very relevant page.

3. 8 Sitelinks in webmaster tools, but only 4 show in our search

That's not unusual. Google may show the others on some different searches.

Yes, the canonical tag will work across domains: http://searchengineland.com/google-supports-cross-domain-canonical-tag-32044

That's a bad thing. Use an alt tag instead. See http://www.youtube.com/watch?v=fBLvn_WkDJ4

You could use canonical or 301 redirects.

Aye.

Oh, and hey! I just noticed I know you from NOLA.

I would be more inclined to move it to a subdirectory on the stronger site.

You could try: http://validator.w3.org/checklink

I would just leave the old links and start building new, good links.

I would double-check that their site is clean and remove anything poor, though.

I have been able to get a couple domains ranked for the same (low to moderate competition) keyword before. They had same whois and server.

That's strange, but I'm not sure it's cloaking. Looks like they are using Javascript to display the product as part of a larger display. If JavaScript is disabled, the product just shows without the larger display of other products around it.

I would consider either to be fine.

So somebody else hacked websites to place links to your website? Crazy.

I doubt you'll be penalized for the links - the links will probably just be discounted.

I would try Elance or Guru to hire a freelance writer.

It is only really required on the non-canonical urls, but it's often placed on the canonical page also. It doesn't have to be, though.