A/B testing is always there, but I'm assuming the site is new and doesnt really have much traffic yet, I can't really say specifically answer that. So it's more of a preference as it's normally the one that brings in results for me more often than not. Then I'll test from there with the traffic/rankings/ctr.

Heck, I'll just imitate Zappos first if I need to then test from there. lol

This is subjective but yes, I almost always opt to have the company brand in there.

Andy and Alan covered what you need to do. One more thing to keep in mind, check the traffic, you don't want to lose those spot in the SERPS. You might want to consider fixing up the subdomain if it gets you conversions and traffic.

Like they said, compile/export everything, combine then remove duplicates and insert to the tool of your choice, like link risk, link detox or even rmoov if you want to contact these webmasters

Be sure to still check the list since it's never 100% right. Some good, natural links can be classified within their calculations of bad urls.

Like Tommy above just said but you might have a reason for doing the homepage as the landing page so just noindex it, assuming they are just direct traffic landing pages