Shalom Uvracha, My sister in law will be staying by us (myself and my wife) my wife is out to work very early and I do not get up so early, which will mean we are in the same house together when my wife is not home (at least for a period of a few hours until one of us goes out) what is the Halacha?

Shalom U'verachah, There is definitely a problem of yichud in this case and the way to deal with this would be either that you get up early and leave with your wife or if another person can have unannounced access to the house where you are. For example either to have children staying in the house with you or to have a neighbor who has a key etc. Kol Tuv