they would've been 1 game back of the Niners with two to play and would've owned the tie breaker because they would've swept them. I don't remember the Niners schedule, but maybe that pressure would've resulted in a different outcome. It is doubtful, as that was a great Niner team (I think they were first in the NFL in Offense AND Defense), but you never know.
As to their record in the NFC, I think 12-4 would've been the 2nd best record in the NFC...not sure how that would've affected the playoff seeding/matchups, but as you said they surely would've played at least one game at home, which could've made a difference.
While those two wins were a great underdog story, being on the east coast for 2 different games before coming to SF was brutal. They were surely exhausted and if I remember right were dealing with quite a few injuries.
There was alot to be proud of with that team...they fought to the very end, and if not for one of the all time great teams playing in their division, they would've had a legitimate shot at a super bowl.