Aside from the two answers you gave on the difficult Rashi (Bamidbar 9:10) , I heard a third answer: Rashi meant that although a person can have and eat chometz on Pesach Sheini but still he can't eat Chometz with the Pesach Matzo umoror together, because there is no room in his mouth for more food. Frankly, the two answers you gave are much better, although each one as a difficult point; The Minchas Chinuch says that Rashi relied on a drasha, however our gemara should have said that drasha, while the Shach reads Rashi with a punctuation very differently than the one we normally would read it with, but which resolves the problem very conveniently.
Gut shabbos Tizku le-alfei alofim miztvos. Nosson Munk
>> 1) THE ISUR OF CHAMETZ ON PESACH SHENI
QUESTION: The Mishnah discusses the ways in which the Korban Pesach Sheni
differs from the Pesach Rishon. One of those ways is that the Korban Pesach
Sheni may be eaten while Chametz is in one's house. Does that mean that
there is no Isur of Chametz whatsoever on Pesach Sheni?
ANSWERS:
(a) RASHI (Bamidbar 9:10) writes that Pesach Sheni differs from Pesach
Rishon in that on Pesach Sheni, "one may have Matzah and Chametz together in
one's house... and there is no Isur of Chametz, except with him while he
eats" ("Matzah v'Chametz Imo ba'Bayis... v'Ein Isur Chametz Ela Imo
ba'Achilaso"). That is, the only Isur of Chametz on Pesach Sheni is to eat
the Korban Pesach itself with Chametz. One is allowed to have Chametz in his
home, though.
The MINCHAS CHINUCH (Mitzvah 381) challenges Rashi's explanation and leaves
it unresolved. He asks that there is no source at all to teach that there is
an Isur Chametz while eating the Pesach Sheni. The Torah only gives us a
Mitzvas Aseh to eat a k'Zayis of Matzah with the Korban Pesach Sheni, but it
never forbids eating Chametz with it.<<
Thank you for your suggestion to answer Rashi! (The wording of Rashi, though, implies that Chametz is Asur and not just that there is no room for it. Also, the wording of Rashi implies that it is only Chametz which is Asur, but not fruits and vegetables, but according to your suggestion, fruits and vegetables also cannot be eaten.)