habit

If I understood you correctly, you are actually saying that after three times we know that we should treat something in a certain way. The question of whether it is a sign or a reason is the second stage in which we explain why we treat reality this way and we choose the story that is more likely in our eyes – In the bull of the due date, for some of the first it is a reason, while in the case of a small woman it is a sign. Although according to this explanation there is room to doubt the latter's words in the Maharam and Raph dispute – According to this explanation, it is possible that even in the bull of the due date itself, sometimes we will assume that the plausible story is a sign and sometimes we will assume that the plausible story is a reason. For example, if our Rabbi Peretz believes that approximation of hits is preferable only if it is a sign, then it is possible that although in the case of distance of hits there we have two options (both a sign and a reason) he will assume that it is a habit, in the case of approximation there there is only one option (a sign) he will choose it in order to interpret reality. So it cannot be said that Rabbi Yehuda accepts Ram's line, but rather that he believes that the holiday's ox is a reason, since this is not a polar disagreement and this is only a second stage in which we choose the more reasonable interpretation of the event, and here the only option is a sign. So what did Rabbi Yehuda and Rabbi Meir disagree about, in the context of Darbanu Peretz?

Indeed. Not only should the latter's words be doubted, but as I have shown, they even turn the methods into their own.
The disagreement between R”M and Rabbi Yehuda is apparently over a question that concerns the appointed bull, and not over the assumption of G”P. For example: Should one assume three days of striking or three striking? Incidentally, it is possible that one of them believes that the assumption of G”P is only a sign or only a cause (and then disagrees on the issues that link the different cases to each other), but I argue that this is not the point of disagreement between them.

What is the logic behind Rabbi Yehuda's opinion of following the days of the strike and not the strikes?

This is the usual logic of the three-fold assumption. If it strikes on three days, it will strike on the other days as well.