To notch the siding to fit the trim atop the door, take the measurement of the length and the location of the trim. Use a jig saw to make this cut. Set the notched log into place. Nail into the tongue into the wall stud.
From this point, one more full log is secured over the door. The rest of the third wall -- and the full fourth wall -- is simply an installation of straight boards.
To create the wall shelves, use the chop saw to cut 4' long sections of log siding. Cut two 4' standards from 2 x 4 stock. Finally, cut 1" dowel rods to 7" lengths.
Place 2 x 4 standards on the wall 2 feet apart. Secure to the wall with 3" wood screws. With one screw in, check for plumb, then attach at every high point on the rounded log siding.
Use a 1" Forstner drill bit to drill four holes on each standard. Each hole must be 3/4" deep to hold the rods. Next, apply wood glue in the holes and the end of the rods and insert into the holes. Tap into place with a hammer as needed.