I think the important thing to remember, when talking about Dr. Jackson's outlandish theories, is that he could be wrong. But then, he could be right. We simply don't know for sure - and we certainly aren't in a position to state that he's wrong. Remember; even if it's educated guesswork on his part, Jackson is probably far more educated and experienced than any of us and so what right do we have to dismiss his theories?
That the Aliens are hundreds, if not thousands, of years ahead of us in terms of science and technology, then, yes, it is highly likely that they can replicate both human organs and whole human bodies. There may be some circumstances where a whole body replication is preferable to transplanting organs (replicated organs or otherwise) and there must surely be plenty of occasions where a new heart, liver, set of lungs, is sufficient. When it comes to replicating entire bodies, maybe the Aliens have a set limit on the number of times a body can be replicated - the limit may be self-imposed or just impossible to exceed. Imagine if there were 10,000 exact duplicates (or doppelgangers !!!) of yourself living on Earth. How likely is it that you'd ever meet one? Quite unlikely. But if there were 100,000 or 1,000,000 it would be much more likely.
As for the whole B142 conundrum... sorry, I don't buy the whole installing an Alien engine block into the space probe. But then, I don't buy the fact that the B142 would have been able to keep up with the UFO and reach its home planet and then send back images that take three or four months to get here. Close Up has some nice moments, but it needed refining and at least one more re-write to iron out all the flaws. It could have been done, but I guess they simply didn't have time. The '1984' and '1981' comments in Computer Affair and Survival respectively are just another example of this. I say, don't try to explain it and definitely don't try to contradict it. There's enough re-writing of history going on at the moment in the world without adding to it!
UFO is far from perfect... but it's perfect as it is.