Hello Christy - thanks for the kudos on my version of the Stink Veg/Cloner unit! The rubber seal is EPDM weather seal - I forget the exact specs. I did post regarding this. No leaks at all - until the seal wears out - I replace it after a couple sessions.
My netcups do not leak at the lid... this is due to the postion (height mostly) of the spray bar and having just the right amount of water pressure - to keep from blasting the holes. If the water is coming out of your holes - it will drain back in too! I doubt you will overflow - but keep an eye on it! More importantyl, you don't want the stems to be sitting in water as this can cause rot. Once the roots get bigger, they cut down much of the water flow from the sprayheads - this will also help reduce water leaks at the plant sites.
Thew grommets are in the electrical aisle... I think they are 3/4" - you drill a 1" hole. Watertight fit - wash the grommets - then use a little dish soap to install 'em in the holes