Well done Nickec, I will be following your progress with great interest.
I have often thought that a Gy6 engined scooter would make a good donor, the problems I encountered with brake and gear linkages are already solved.
If you want to lower the seat, there are any number of different manifolds available. It may even be possible to reverse your existing manifold so that the carb faces forward.
Have you considered using a car roof box as a basis for full enclosure?.
Available in many different shapes and sizes.
What are your thoughts?