the mortise can also be cut with a chainsaw, IF you have the experience. I have done this a fair bit, esp with braces.
For using a free hand drill you can also screw a straight board on to the end of the log, that is parallel to the mortise. you will be able to use the board to sight the drill bit.

a chain mortiser can also be used, if you have one.
we regularily bolt our mortiser to a plywood base to do stuff like this.