The bottom of the tank should NOT touch the table! 1/2 inch is the highest you should have to go to prevent the glass from bowing far enough to touch the stand you put it on. 1/4 inch might work but I would make it 1/2.
The strips are on top of the sides, not inside them. They do touch each other and are siloconed at the seems, or should be anyway. The strip from front to back in the middle will be on top of the other strips in the middle of the tank or the strips can be cut so they are all level put together like a puzzle. I guess it really doesn't matter which ones are longer, across the front or across the sides. All the pieces just need to cover the edges so they have axtra support and a place to put the lights. I would also make sure I have a top to the tank that covers the entire tank.
This does pose a problem for a HOB
filter. I would "guess" that you can leave an openning in one of the pieces of glass across the back the width of the HOB
filter or the area you need for the tube of a canister filter. This should not affect the strength of the glass. Just make sure you make the tank to support whatever you want to do in the tank while reinforcing it across the top.
Acrylic can be flat on the desk.
One more thing, when I build my tank, to accomodate for easier cleaning I will slant the bottom so it tilts toward either front, back or one side. This gets all the debris to one side and helps the filter get it all sucked up.
Best piece of advice, build a 20 gallon tank first so you know what you are doing before building a monster. I will build 3 tanks, progressively larger, 35,75-100 and then my huge tank whenever I get the room to actually handle it. Will post a drawing, very rough one in a couple hours.