Company A purchased another company and merged the plans effective 1/1/03. Do you look at what the individuals' comp was from the previous employer during 2002 to determine if they are HC or are they treated like a new hire?

It depends on the form of the transaction and how it affects crediting of service.

If the plan came over, does it really matter whether it was a stock or asset deal? My understanding of the informal IRS position is that the comp from the target counts if the plan comes over. I don't think there is any authoritative answer either way on this question, though.

I think that its clearer in a stock deal than an asset deal.