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Test them on a dummy site if you have the budget, or on some pages that already link to you.

Are we talking spam automated links, paid links, or something else?

If it's spam auto links - they'll get banned sooner or later.

If it's paid - read up on how to minimize the risk and jump in. Intermediate sites are one approach.

If it's paid - point out the risks of penalties to people selling the links. "OMG, my site can be banned. No wayyyyyy! Why didn't they say so! Nofollow!"

1. Keyword difficulty is useful to sort equally-well converting keywords on PPC and see what to SEO for first. ID the low hanging fruit. 2) I just finished a link analysis training with a client. Honestly, it's shooting fish in a barrel with OSE. And if you can answer WHY you're getting links and from WHOM, you can expand on that and rank #1.

Has it penalized you, or just the links got devalued? Are you ranking for brand KWs? If so, don't waste time - keep building.

Would it not be easier to get the lead gen / advertising / monetization stuff to transfer over to the other domain as well? Presumably if its a choice-of-where-to-advertise thing you can influence them to see the light; if it's that B has a stronger brand / greater ability to convert, then perhaps a moderate rebranding to tie the two together (and thus use testimonials from A on B can work?) Easier to control logos and colors than google's algo...

The question that matters is what does SEO need from URLs?

1. That they be static.

2. That they feature your keywords.

What does Big Commerce do?

1. Provide static URLs (at least, based on what you've shown; I'm not a salesman or anything and have no affiliation)

2. Features product name (which presumably you control, and can thus include long tail KWs).

Granted, it's slightly less easy to type out the product page URLs for anyone wanting to link (they need to remember the caps and .html) but that's the least of your issues. I'd imagine you can just set up a 301 to make the urls typed in redirect if they get the casing wrong.

Lastly, regarding custom URLs, consider scalability. If the store succeeds ... are you really going to give each product page a custom URL manually? Not likely... So it's not that important.