You can use this jig setup for both the alaskan mill and the mini mill. Irregular shaped logs, with branches will not hinder you from making the first cut. After that, you use the surface of the first cut for your next cut. That means your first cut must be a good one.
This is a 20' 6" long white pine log that is 30" or more in diameter. I cut at least 6 good slabs, full length. I got $30 a linear foot for the 2" and $50 a linear ft for the 3". I actually used my 5' Alaskan mill on this tree.
This picture shows how I modified the jig for easy adjusting. There are holes set apart about 3" for the pin to be inserted and the eye bolt can raise or lower the sides of the saw to get a level cut. The long slides are barn door rolling tracks.
This picture shows how the mini mill can be used in conjunction with the Alaskan mill to make the first of two cuts that will remove a perfect 90 degree piece from the back of a log that was then used to fit over the corner of a wall that turned into a hallway. The aluminum angle guides are screwed to a 2" by 8" piece of treated wood.
This picture shows how you can level a cedar stump, to be used as a base for a glass table top. Since I did not have a level surface to start with, I made another jig, using 4 leveling jacks for scaffolding with sections of 4X4 beams with holes cut in each end. By leveling them and placing the stump on them I could use the Alaskan mill to give me a perfectly level top to the table with one cut.
This is an 066 with a 3" Alaskan Mill set up to level an irregular stump for a coffee table. Notice I have wedges under part of the stump as this is the first cut. I then flipped the stump over and leveled the other side.