Is the bottom end of the two motors the same, other than crank and con rod?? I have no idea but that sounds kind of unlikely...? Could an XT350 cylinder even fit down into the crank case of the 250? Also seems very unlikely, to me, at least.
If it were possible though, that could be a cool conversion. Even more cool could be a "factory" big bore "kit" with this idea, on a newer, fuel injected XT. If one could just change the parts you mentioned, and then basically plug 'n play the 350's cylinder, and then get a fuel programmer... I'm just having pipe dreams at this point lol.
I am not an engine builder, but the more I think about it, the more ludicrous and impossible this seems