1. I seem to remember that the Mexicans were very unwilling to cede as much as the Americans demanded OTL. Now, I still don't know why they'd want to keep Baja, since it's largely unpopulated, not very strategically vital and resource poor. Easiest Handwavium may be that the Americans offer to pay more money. I guess the first butterfly is this: does the state of California get all of it or will California get split into multiple (maybe three?) states? I have a slight tendency to think that some kind of split may occur, which is bound to cause all sorts of probelms in the crises of the 1850s and the build-up to the Civil War.
2. Two potential butterflies: 1) as above, the addition of more land might cause more ruckus about free/slave states. Smaller chance, however, since if gold rushes etc. happen on schedule, the Pacific Northwest will not be state-worthy until after or just before the Civil War. 2) Does the US still buy Alaska? The former is tricky, but the answer to the later is I think yes. OTL, the Russians sold it to the US because they didn't want it going to the British, IIRC. TTL, the British/Canadians will perhaps have greater reason to want Alaska (Pacific ports), but the Russians all the more reason to deny their wish. Also, if Canada does end up with Alaska, but without BC, then Confederation with Alaska may be harder (if Alaska makes demands like those BC made, concerning rail access to the East; which of course they might not do, since it's very lightly settled). In any case, there will be large butterflies for Canada without BC, particularly as regards Confederation. The Canadians will have even greater reason, OTOH, to resist the US earlier so Confederation may occur sooner.
3. This gives some answer to 1 and 2.1 above, since it allows for example, the admission of paired states from the Western Lands. A State of North California/Jefferson around San Franciso; and a State of South California/Jackson around LA and San Diego, the latter possibly open to slavery (IIRC, Southern California contained some CSA sympathizers). In all, however, this may make the Far West a more hair-raising theater for the Civil War, if it breaks out as OTL.