To replace the Jews in local economies, the Germans created trade schools where the "natives" were going to learn all the necessary skills.
How is that not a waste of resources?
Actually, the capable-of-work Jews were usually spared - it was called "selection."
So, even in this case, nothing was "wasted."
The whole selection process itself was a waste of resources to begin with. And that's before we even begin to look at how taking people out of work they were skilled and expert in, transporting them elsewhere, retraining them, putting them to different work - work they were likely neither good at or motivated to do well, working them to death and thus having to repeat the cycle endlessly, benefits the economy.
The Final Solution wasn't a continuous process, but rather two (relatively brief) bursts of activity.
That is undoubtedly the case, but I am not sure what your argument is here. It sounds a bit like you are saying (moral issues aside, of course) that since most of the job was done and significant resources had been applied to it, it was worth committing a bit more resources to finish it. That is a common fallacy in economics. The reality is that waste is waste, whether on a massive scale or at a more modest one. The only 'correct' response to a wasteful project is to terminate it, regardless of how much resource had been committed to it in the past (ie not throwing good money after bad). Someone keen on prosecuting total war efficiently would not want to continue waste however (relatively) small it had become.
Unless all you are saying is that stopping the Holocaust in July 1944 would not have saved many Jewish victims, because most of them had perished by then. That is, sadly, true also, however not really an argument for the continuation of the Holocaust. If anything, it is a diminishing returns argument for the opposite, that could even be used to persuade ardent believers in Germany.
Most of the people killed in the death camps were Polish Jews, already weakened by 2+ years of ghettoization.
Itself a massive own goal and pointless waste of resources.
Killing them, beyond the fact that it was an atrocity, contributed to alleviate the Grossraum's food shortage at the margins.
How so? Did it increase the amount of food available? Actually it merely reduced the manpower that could be used to make more food in the future. From an utterly amoral point of view this is a classic example of a problem that solves itself without any interference or effort. In other words, iterfering is a complete waste of resources. And also, more often than not, counterproductive because it is an argument based on the fallacy that the amounts of food, money, jobs etc are fixed and that therefore if you reduce the size of the 'herd' there will be more for those that remain. As time after time has shown, following this faulty logic has led to disaster (dare I mention the sparrow holocaust in China?).
On another train, of thought, RedTelephone is right. However deluded in that respect the plotters might have been, their aims were, among others, to get the Western Allies on board. I doubt they would have been unaware that continuing the Holocaust was not going to help in that endeavour.