Plexiglas is a trademark name for a particular brand of clear acrylic sheet. So, yes, your top is the same as plexi. I'd keep the light at least 2-3" above the top to keep it from bowing from heat produced by the light. Even regular fluorescents can easily burn at 80-90 degrees F. If you're having a custom hood made, that shouldn't be difficult, though.
:my top will be acrylic, im not sure if thats the same as plexi or not.
:i did think about some not being able to run off a timer. i will be suing a timer so that is something i will have to look into.