Yes, the Munich 95 manuscript is censored, but not in a matter as exhaustive as some later manuscripts. For a list of Jesus-related censored and uncensored passages in the Munich manuscript and several other manuscripts, see Peter Schäfer, Jesus in the Talmud, pp. 131-144 (link). See also David Instone-Brewer, "Jesus of Nazareth’s Trial in the Uncensored Talmud", Tyndale Bulletin 62 (2011), pp. 269-294, which I think will also be useful for your studies. Consider also googling the words "Munich 95" and "censor" or "censorship" for more discussions on the matter.
As I mentioned in the comments, unfortunately we don't possess any Talmudic manuscript that hasn't ever been altered. We don't have the original Talmud copy. Rabbis, Talmud scholars, and historians spend years trying to unravel millennia of variant traditions, textual evolution and scribal errors to try and recreate the original text and decipher the original meaning of the Jewish sages (I myself have attempted that with regards to one particular passage in Bavli Shabbat, and I'm well aware that though IMO it's well-argued, it's just a hypothesis).
I can refer you to some studies on the textual tradition of particular tractates, though I believe most of these are in Hebrew.