In the case of an out of square post (also roughsawn), if I want to house my intersecting beams on the non reference faces, should I measure in equal distance (say 7.5" on an 8×8") from the reference faces instead of measuring in 1/2" off the non reference face.
Yup. Although you should always, only be measuring or squaring off of the reference faces. It's bad timber frame juju to do otherwise. Sounds like you need an Al Borneman layout tool (from the TFG). It'll save you epic amounts of time in square rule.
If this is the case I'm also assuming I can't use a skill saw to the full depth to cut the housing if the timber is out of square by a 1/4" or so? My thinking is I will have to cut it to the shallower depth of the two sides and then work it down with a chisel so that each beam comes off of the both sides of the post in line with eachother. I'm also assuming this will require shimming my mortise machine so that it will be in the same line as reference face mortises?
Yup and yup again. Sometimes it's just easier to handsaw or chop it by hand.
Another question, If I want to house my braces in the center of the post on these out of square faces, what's my best solution? I'm considering shimming a router template in the shape of the housing joint to be parallel to the reference face and routing it out but would welcome tried and true solutions.
Yup again again. You could also chop it by hand. And yes, you can reference off a framing square. Jim Rogers used to make a doodad to connect two squares together, so that you could check things on non-reference faces. You can also just use stair buttons to connect two framing squares together.
