1) I would use glass for the baffles. Glass to glass bonds better than acrylic to glass. The pieces of glass will be cheaper also.

2) Not sure where your drain will be. Some designs raise the 'a' and 'c' pieces and inch or two off the bottom so that water goes under 'a' over the shorter 'b' and under 'c' for bubble reduction.

3) Sounds reasonable to me.

4) If your skimmer and return pump fit comfortably in their respective areas and you have easy access to them it should be fine.

Just my thoughts. HTH.

Ed