Hi Deborah
Thanks for asking - I love to talk about it : angel
So the listing in Science News March 2004 - Vol -165 about modern man's DNA and the Neanderthal is a stretch?
Yes and no

It is true that the neanderthal DNA does not match ours, but we still know very little about the difference. It is a process of reading the three-billion-letter genome that makes up neanderthal DNA. In 2006 the main research group on this announced that they had deciphered one million, last year another Germany-based research group announced that they had identified about 70 million letters. That's about 2% of the whole genome. Based on that, conclusion made in 2004 would be a stretch. What they see so far is that for most of the sequence there is no difference between neanderthal and modern human DNA - the difference makes up only 0,5%.
There are huge problems working with ancient DNA. Especially contamination. Ancient DNA in fossils is very faint and, obviously, with only a 0,5% difference contamination by modern DNA can be almost impossible to catch. Let alone the fact that modern human DNA differs individually by - I think - about 0,35%.
Basically, there is still a long way to go before we understand neanderthal DNA. When the genome is fully identified it's also worth remembering that the sample size is small and that neanderthal DNA also differed individually, so there is a discussion of how representative the genome actually is.
About chromosome 2 -do you know anything about that?
No, I must admit that I haven't heard of that before. However, as far as I can understand it implies that the neanderthals and h0m0 sapiens interbred. That is - at the moment - one of the big questions that are unanswered. Problem, again, is the sample size. It is generally accepted that modern humans and neanderthals did not interbred. The remains of a child, a young boy, from Gibraltar was long believed to be a hybrid, however the arguments have yet again been questioned. Another scull from Germany was also praised as the proof of interbreeding, however new datings prooved that this was not an early modern human, but from the bronze age.
For parallels we usually look to the animal kingdom. Here we can see that different races of the same species are able to mate, however their offspring is usually infertile. Some people suggest that this was how the neanderthals became extinct. That they simply interbred with modern humans bringing infertile kids to the world and thus, eventually, died out. I don't think that's an argument that explains much else, but the fact that the neanderthals died out.
Eta: I just did some research on chromosome 2 and I did misunderstand a bit

The chromosome 2 is viewed as the result of a fusion between two ancestral ape chromosomes, so it goes much further back than just neanderthal and modern humans. But in that case, Braden is correct. It did take two species to make chromosome 2
