first of all thank you for answering. I don't know, maybe it is just me, but looking through the Grundisse I had the impression that for Marx what comes first is the free play of human creativity, living labor. His discussion of the "civilizing power of external trade" seems to point out that it is only through trade of surplus product that human products become quantitatively comparable on the base of their exchange-value - as opposed to being only qualitatively comparable as use-values. Independently from exchange the object created by our own labor is only valuable because it is useful, not as embodiment of an abstract "socially-necessary-labour-time". We can compare our home-made trinkets only qualitatively, not quantitatively. So first is human creativity, then is trade and the commodity. And what's next? Then, while all of the product of social labour comes slowly to be commodified ("not even the bones of saints can resist this alchemy"), we have primitive accumulation.
My problem with primitive accumulation in Capital is that it is something that Marx leaves at the margin of the argument, as if it was an appendix. We have to "assume the existence of a primitive accumulation". One can not understand why primitive accumulation happened in that specific moment in time and in that fashion reading Capital. It is a story of the original sin, it is not explained either theoretically or historically. Why did primitive accumulation starts? In the Grundisse you have an explanation, more or less explicit, which says it has something to do with the effect of growing English foreign trade with Holland. One could also think of a technological reason, and I guess there must be also that in Marx somewhere.
But I don't think that saying this, saying that also primitive accumulation must be dialectically explained, is to state that there is an identity between the historical content of the book and the exposition of its contents. Indeed I think Capital can hardly been thought as an historian's book, although clearly there is lots of history in it. The exposition clearly does not want to be historical. So, I am not sure, but I think I really agree with your comments on "On the Method of Political Economy".
About the mode of exposition: Marx is trying to explain "the whole movement of capital" which "seems to turn around in a never ending circle". The explanation of that circular movement takes the first 25 chapters (all of the book but 70 pages). The last part, on primitive accumulation, poses two theoretical arrows at the opposite sides of the circle of capital. One very real, violent and historical - that is the moment of primitive accumulation - the other still to come, a possibility which Marx wants to indicate. I think the purpose of the last part of Capital is to draw these two theoretical arrows. That's why Marx doesn't go on explaining the origins of primitive accumulation itself. In my understanding the origins of primitive accumulation seem to lay in commerce, "external exchange" and the rise of commodification. I don't know if you would agree with that or if you see it as problematic.
Maybe on wednesday we will end up having a massive group fight on the correct understanding of primitive accumulation!