Mark,
1) I would use bottom right; all my gutters start on the far left side and I use bottom left for those. Also, if you have this drawn out on your layout, why not do a simple chase and see what it looks like on your model.
2) Your rectangular sections sound just like a window model - 2 equal sides and top/bottom equal. Setting up as 4 individual models is fine too since you can create different effects on each side.
3) So many options you can do - single line (just like you did); a window model or a custom model. It really depends on what effects you want to achieve.
Once again, I suggest create your models, and add a couple effects to them and see what you like. You may end up with all 3 types and use different effects for parts of your song.
Oh, if you use the single line, also create you a group and include all 4 sides - another option to choose in sequencing.