Windows. Clear Plexiglass on top and bottom, and in rear "quarter windows". 3/32" thick, a full 4' x 8' sheet is more than enough for everything. (Just top windows can be made from a 4' x 4' sheet)
Plexiglass is gas resistant. Side windows open upwards, right under the gas drain. Lexan is easier to work with, but in this case Plexi is used to prevent fuel damage to the window.
Plan is to make the windows easily removed and replaced. Skylight Lexan expansion/contraction of of approximately 4.5 x 10-5, or about 0.0018" over 4' span per degree. Over a -20F to +110F about 1/4"... so 1/8" per side expansion/contraction. Should be pretty clear why you don't want to bolt the skylight in tight, but use larger screw holes, and allow for movement. Cessna makes a sealing tape that allows for movement (no hardening).