Perhaps this is oversimplified but what I do first is remove the damaged deck and recreate it's correct shape. I simply run a steel scale up each side and trace where the tips should be onto a sheet of cardboard. I cut the tracing out and the repair the deck by replacing the damaged piece. If it's contoured you will massage the parts to fit as you go. If you continue the lines of the stem and the attached planking you can very closely approximate the required stem shape.
Once I have the deck repaired I put it back in the canoe and do something very similar to figure out the inside rail locations. I work back far enough to get a nice splice for the replacement pieces. I try to keep the splice within the length of the deck in that the deck then helps to reinforce the repair when you screw everything back together. You can rough fit the rail splices to get an idea where your stem splice will need to reach. This is not an exact process...every boat is a bit different since these parts (decks, stems, rails, planking) are all fitted during assembly and age and damage often results in more variation. They often vary end to end...and only the builder will ever know. The one I am currently working on is so different end to end that I have had to remake my stem form to get the correct shape for the outside stems. Your eye would never be able to tell.
I looked at the Mike Elliot links you attached and they look like almost the same thing I do... You may also make the stem splice first and then make the rail splices.
The one thing you should pay some attention to as you pull it all together is making sure that your stems are vertical and that the decks and rails are centered. You don't want to put a twist in things. You can try to eyeball this but I find it easier to level the canoe (rail to rail) and then position a laser level sitting on the bottom of the hull projecting a line on the stem. Center the stem to the line as you tie everything together.