Dylan, the best way to get even cheeks and shoulders is to lay it out with a marking knife.
It’s a well thought out jig, but sometimes it is quicker (and safer!) to do certain tasks by hand. The time it takes to design and make a jig, do test cuts, dial it in, etc. you very well may have them all cut with a handsaw. Plus, if it’s a one off jig, you have all that time invested and never use it again.
My point is hand tool work can be just as accurate, in some cases more accurate, than a machine.
Either way you go, don’t try to cut the tenons perfect off the saw it’s too stressful and very difficult to do. Cut them big and use a chisel, rasp, and/or block plane to tune them up.
Cut the mortises first and fit the tenons to the mortises.