I'm working on my deck design, and sometimes I feel like I get lucky when doing extruded cuts, meaning I am clicking what I think should be clicked and the cut works out for me, haha. I am doing these in the assembly, as not to change all the parts in my configuration. If you look at my picture, I managed to cut the studs parallel to the rafter without issue, but obviously the studs and rafter are still taking up the same space, so I have to cut that out. I have a hard time telling what plane to start the sketch in, which entities to convert, when to convert entities, when not to, etc.
Since you've already cut the end of the rafter you can create your sketch on its face...
...and choose "Up to Surface" as the end condition, selecting the opposite side of the rafter. Again, select the studs for the scope of the cut.