I don't have much personal experience with round logs. So I'm only saying how I would approach it.

My first goal would be to envision the timber in the log. To do this I would start with a log a bit longer than the original dimension. I would rough cut square both ends as close as I could by sight. Then I would string a line from one end to the other in the middle of the top. This is a reference for the centre of the log. It will be a set distance above the centre point of your stock. If you need to offset this line at one or both ends with a plywood disc or square that is fine. Depending on your stock you might want to also snap a line. At this point you can square down off this line and left and right and establish a square end cut in relation to the line.
When your ends are cut square you can establish any point on the log with relation to an offset string line. Depth and mortise location can be determined by plumbing or levelling from the line.