I'm not going to get too much into this, but just lay out a few areas where your thinking is flawed.

First and foremost, you're making an initial mistake by using misleading evidence from what seems like a suspicious source (Nexus Magazine (2002)), and then making huge assumptions (Your "Starting Posits") to try and incorporate the views into a plausible theory.

I'll go through some of the questionable evidence:

1. The article states that there is no evidence of an evolutionary connection between flowering plants and their predecessors. This is false, here is an article (with a sourced paper from 2013) showing evidence to the contrary, a 'genomic doubling' : http://www.iflscience.com/plants-and-animals/origin-flowers-has-been-discovered/

2. The author has this strange idea that humans couldn't eat wild grains for years because they were too small and hard, he says they managed to miraculously change them 5-10,000 years ago. In fact people were eating wild grains well over 20,000 years ago. He doesn't take into account any rational explanation for how these grains evolved (such as ice ages/climate change/mutation/environmental change etc.), he just jumps straight at the "god/alien intervention" theory, as you have.

3. The article make more assumptions, that what it calls "directed crossbreeding" is an incredibly technical process, that couldn't have been achieved by "primitive barbarians". In fact, this crossbreeding would have almost certainly started in the form of artificial selection/selective breeding, and is actually a very simple and easy concept to observe. I have no doubt that primitive humans that were capable of planting crops could have started selective breeding within a few generations. If a beneficial mutation occurred in a plant (higher yield/larger fruit etc) then this knowledge could have been applied straight away to exploit the mutation, creating huge amounts of crops even within a single human generation.

Another relevant theory (which I think you touch on in your post) is the population explosion and more sophisticated behaviour in humans that occurred about 50,000 years ago. Is it not much more plausible that this increase in population, intelligence and social sophistication allowed humans to start experimenting with plants, noting which ones grew well in certain conditions etc? There is strong evidence for their hunting techniques improving at this time, and if we look at some ancient tribes, they have incredibly specific knowledge about the plants and animals that inhabit their environment.

So to sum up, although your theory is certainly an interesting one, I don't believe there is anywhere near enough evidence for it. You are showing strong signs of confirmation bias, trying to fit selective evidence and theories into what I suspect is some sort of religious/supernatural worldview.