You would be removing the existing ballast, the fluorescent sockets and wires to the sockets. The input wires, should be black and white with a green ground would go to the input (120V) on the new transformer.1) Will I still be able to use the fluorescent lights and ballast on the bottom? Yes no changes to the bottom.
2)Does this company not provide bezels? Not that I could find but you could call them to ask. Something like this http://www.ebay.com/itm/MR16-PAR20-...90936?pt=US_Wall_Fixtures&hash=item414def1f18
3) The first item linked, do I get the 20 watt or 60 watt? They are 3 watt bulbs X 4 would be 12 watts so the 20 would be ok. If you later wanted to add corner strip lights or logo I would get the 60. I put a 150 in mine but I overkill everything.
4) You mentioned taking the 2-wire input from existing ballast and connect it to LED transformer. Are you referring to the ballast that still works for the bottom lights? Because the ballast on the top is bad.
Here is what mine looks like. My lights were a bit larger than standard MR16, liked the blade look to these and the big heat sinks (overkill). I had to engineer my own way of mounting.
You may also want to wire in a dimmer here is just one choice. http://www.superbrightleds.com/more...lt-dc-single-color-led-mini-dimmer/1082/2573/