Which material are you using to build it?
I suggest using a 24'' T5 fixture and tube over the basking area. I also suggest putting vents low on the cool side and high on the warm side to allow for convection ventilation. There are metal gutter guards that wind up looking pretty nice as vent covers. Are you going to do sliding doors or a drop down? If you can swing the extra cost of glass vs plexiglass I'd do it. it will wind up being more scratch/scuff resistant and look better in the long run. Since your ceiling will be fixed, you may want to set up a dimmer so you can fine tune the basking light. A dimming thermostat would be best but you could rig a manual dimmer to the basking fixture and have a dial on the outside to make it easy to control manually. You could mount digital displays for the thermometers to the outside too so you can see the temperature gradient (hot/cool side) at a glance.