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I literally just got off the phone with Jake over at Virante (in NC) and one thing he was mentioning was Anchor Text penalization and that it occurs on the keyword level. If/when you get dinged on the keyword level and presumably with 1700 products that could be some serious keyword cannibalization. Try just using the/a brand name URL [http://www.youdomain.com] or [http://www.afilliatesdomain.com] when utilizing Anchor Text. Google will not penalize you on a "brand level" whereas they might for being hyper-prolific with "Green Widgets" or some other generic popularized keyword (phrase).

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Good luck and good on ya,

Cheers, 
Brian

Heyo,

I'd start with OSE and export the data compare it to GWT "Your Site on the Web" tab (specifically the Internal Links as well as the Links to your Site).

Then take a trip down to good old:

• http://www.backlinks.in/

This is a great way to analyze Second Tier Links if the first site contains links with the secondary URL. Also consider analyze the anchor text with this process. Will probably take a bit of elbow grease, but this is a good start.

Good Luck and good on ya!

Shameless Plug: follow me @derZukunft on the Tweeter.

Cheers,

Brian