As far as the "junk" dna, the more we learn, the less "junk" there is. It may be a function of our incomplete knowledge rather than true "junk". I remember a study recently where most of the "junk" in humans and some distant critter was CONSERVED. If it is conserved, it is NOT junk, it just has some use we have not discovered yet. What study are you referring to? And what do you mean by conserved? Do you mean that cells actually go and make sure junk is present? In some cases it is true; there are pieces of DNA that are useless to the body but get copied and put into other places on the genome. It exists solely because the DNA has an aptitude for it, and doesn't kill the cells harboring it. Read Richard Dawkin's The Selfish Gene.
EXACT same genes are found in a given bacteria and humans, but lacking in many types of critters alleged to be between us.
I haven't heard of such DNA. I am not denying it exists, but it may be possible that you misinterpreted the results of an experiment (i.e. there are bacteria known as archaebacteria which live in extremely savage conditions which more closely related to humans than "regular" bacteria.) In either case, I would be very interested in seeing an article about this.
http://www.discover.com/apr_02/gthere.html?article=feat_petri.html
That study tells about the shared genes that are lacking in intermediates. Of course it is full of evolutionary conjecture, but if you look at the substance of the article it is astounding proof for ID. The evo scientists in the study were just astounded, they were not about to consider how much better the ID hypothesis fit their evidence. Instead they came up with wild, unsupported conjecture to explain the facts away.
As far as what I mean by "conserved", I mean that there is a lack of mutations in most "junk" DNA that should be there if man and fly have been accumulating random mutations in their "JUNK" for 500 million years. Our JUNK looks too much alike to truly be junk.
It seems that random mutations are being selected against, so that our junk DNA looks like the corresponding JUNK DNA the fly has (much less).