For these larger pieces, I'm using 5" round stock cut into slabs 1" thick. The benefits of using round stock are the greater strength in the material with the parts holding together better, and with it being round, it makes setup extremely easy. The downside is a material waste since the parts are rectangular, there is a significant portion of the disk that gets thrown away.
I ran into some issues when cutting the parts out where the contour toolpath would snap my endmills when it did the lead-out. Since these parts have flat walls, I'm able to use contour toolpaths to cut it out of the main block; the problem I ran into was with the tool exiting the material, it would pull out to the side crash directly into the remaining stock. Unfortunately, the contour toolpath is a 2D operation, so it only reads the geometry you reference and nothing else.
One solution was to drill a hole down to the bottom to have the tool move into the hole before retracting; the downside is that you have the extra run time with the tool change and drilling. Another solution was to remove the lead-out and have the endmill pull straight up at the end. This isn't ideal, as if there is any vibration, the tool would leave a mark on the side of the part.
I talked to my boss a bit, and he said in Mastercam, the contour toolpath does a spiral down to each step in the same spot; this creates a naturally occurring hole in the side of the part. This got me thinking about what I could add to the contour toolpath in Fusion360 and emulate this same idea. By default, the tool has a short, 90degree angled lead into the contour, but space is a bit tight for the endmill to retract without hitting a wall.
Playing around with the lead-ins and lead-outs, I found that you can change the 90deg angle significantly higher than I initially thought. After setting it at 200 degrees, I got a really smooth double arc that curves in on itself before leading into the contour. This was exactly what I was looking for, and it created a small bump in the side of the contour with plenty of room for the finishing endmill to retract in!
Once I got all the disk-made parts finished up, I set up a jig plate in the vice for each of the parts' final operations. There are a few small features, like holes and small pockets to clear out on the sides of the parts that I didn't have access to in the first two operations. Instead of setting up some soft jaw setup, I'm able to use the back wall of a flat plate to brace the pieces upright and take advantage of a pin to use as a hard stop, thus creating a repeating work origin with each tool set off the top of the part.