The windows, door frame and the door sill were set in a bed of silicone sealant.
The inside gaps were then caulked back to the wood framing.
The bottoms of the windows were not caulked on the outside so as to not trap water if it were to penetrate the window frames.
Window's were purchased with the J channel for the siding already incorporated into the frames.
Door frames were ordered for 2x6 walls with extended jambs and the PVC trim and frame assembly that is designed to not rot out.