We have some ideas, but I don't want to influence anyone, so I'll keep them to myself for now.
This question is mainly about rafter layout, not about sealing the roof from rain, although suggestions/experience related to that are also welcome.
Ground Level View
Crotch Level View (leave it alone!) The board is there just to show the height of the crotch
Bird's Eye View (simulated)
The smaller branches are not an issue, they will be cut. It's the 2 main trunks that need to be dealt with. Based on the location of the trunks, neither 16" OC or 24" OC will clear them.