is the zoomed picture showing the beginning of those files, or somewhere in the middle?
does the error seem consistent as you go forward in time (ie. the 2nd file is always a little ahead or whatever) or does it drift around?
What happens if you try recording from the mpc's multiple outputs into multiple inputs on your soundcard? do those line up then?
And I'm still unclear on the first method you tried,, how did you cut them at the beginning? (you said at the first hihat) ie by eye? Using 'snap to grid'? By zooming in?
Anyway, Im 99 percent sure there is nothing wrong with any of your gear.
Rather you are seeing the normal inaccuracy of midi synchronization.
Its very very common to see errors of +/- 1 millisecond or even more when it comes to midi sync. Mostly this is to do with the Operating System of your computer, they are not well designed for tight signal timing. (Audio is different, i won't get into it.)
In fact, if you told me you had a pc midi interface that was guaranteed to be off by 0.5 ms at most, I would buy that for a couple hundred dollars

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On the upside, the human ear cannot detect so small an error, afaik. I have seen research that suggests 5ms as a threshold, so even being conservative I think maybe 1ms is the absolute minimum where anyone could hear the difference. Phasing, however, is a valid problem if you need to have the same samples on different tracks for some reason...