And adding to that, I'm not entirely familiar with the Naruto continuum, and haven't seen much MST3K(though I've watched enough derivative videos/read enough fan-inspired works to know how riffing works).

But from what I did see, it wasn't all bad. There were some funny moments, like the "When did it take it? Last poker night?" line at the beginning, and the "Unlike the gates of the town, which were unlocked and wide open." bit on one of the later pages, and you seemed to have the back-and-forth of the dialogue down pretty well in most places, but it did have its problems.

One problem I noticed: a lot of references that didn't add to the momentum or humor. Some of them weren't even entirely necessary, like the Starcraft reference that you immediately explain(references are usually intended as shorthand for certain concepts in this context, so if it's something that's easy to explain, the reference wouldn't have been needed at all) and a lot of others were obscure or confusing.
For an example of the latter, I had to look up what the Horseman's Word was on Google while I was reading the MST to get the joke that involved it, and now I'm just confused as to why you assumed that most of your readers would be in the know on Scottish secret societies from the 1800s. By the time I was done wondering, any humor that the joke might have had was dissipated. There were a few other references you made that I couldn't even find Wikipedia pages for, and I'm still lost on what the joke was on those. Like with "Pixy Gale". All I was given from the Google search on that was the information that it was a manga, as well as a few pictures attached to the top of the search screen(unprompted, mind you; I had intended on a Web search) that made me contemplate clearing my browser history.

Another thing: you talk about the canonical details just, at length. Since I don't know the continuum very well, that stands out to me even more. A riffing, as I know it at least, tends to have several brief humorous moments that react to specific flaws in logic, individual lines and/or dialogue to mock, what have you. True, in the video formats I'm most familiar with, it's kept brief to keep from covering up anything else the riffers would like to mock, but it's a good principle in general.
Talking about canonical details, while helpful in determining what the story does wrong, isn't really that entertaining. That's why it's best for recounting what just happened to occur in short bursts, interspersed with jokes, reactions, puns, what have you. I spent most of those asides looking for some sort of comedic payoff, or punchline, or running gag, or something, but nothing came up. Look at the page right after the "Chapter 2" heading to see what I mean there. I'm not going to copy the whole dialogue here, because I made my point and that would be too many extra words.
Addendum to this: Dragging something on too long, even if it's a joke anyone can understand, will make it less funny. This didn't crop up a lot here, but given this writing style, it's something to watch out for.

Oh, and one last thing. You explain a lot of the jokes. Cut that out. I had actually briefly laughed aloud at "Poor Foot. He was a good man once.", and then you went and explained it in the next few lines, roping in more canonical details in the process, and I could feel the laugh die in my lungs. It kind of stung. Sometimes you just have to let a joke stand on its own grounds. You even mention this problem in the dialogue at one point, but don't do anything about it.

I was going to say something else, but now that I'm at this point, I've forgotten what it was. Oh, well. This post is long enough as it is.

I mean… well… I've never really been good with this sort of thing. Or whatever.

The best I can think of is heavy sarcasm on the abusive!villagers. That's it.

Sorry.