roof flashing

I am planning to replace this roof with an insulated warmroof and lightweight tile. It currently has an L shaped box gutter which I want to design out. How would this be done? I'm fully aware it's very complicated but would appreciate and pointers of where to start. Specifically, I need help...

I'm having a catio/patio lean to built and plan to roof with EZ Glaze sheets but I need help/ideas on how I can work around the soil pipe and water seal around it. I was thinking to use the EZ glaze flashing, get them as close the the soil pipe as possible, add V-Seal® pipe flashing or Dektite...