Is the 40 gallon glass or acrylic? If it is glass, you will have a difficult time putting acrylic baffles in it. Mine is glass and had a glass company called Binswanger Glass in Denton cut the baffles. I also had them polish the edges so that they are not sharp. If it is acrylic, you can get pieces cut to size at Regal Plastic off of I35. For glass I went with 1/4" thick. For acrylic I would use 3/8". 1/4" acrylic flexes pretty easy. Marc could give you more info on this.
Do you plan on using an auto top off? If you do, the size of the return area can be pretty small. If the current 40 gallon one you have is drilled on the end, then I would set it up as follows. Tank overflow into skimmer area...then a 3 piece bubble trap made with baffles...then fuge...another baffle...then return. Make the skimmer section only big enough to fit the skimmer. Make sure to leave room to get it out though. My skimmer section is bigger than I wanted, but I have to tilt the skimmer to get it out. You said that you wanted to use an external pump. If so, the area for the return can be small. If you use a submerged return pump, make sure that area is big enough for the pump and plumbing. (get the pump first)
Without knowing the size of this 40 I couldn't even begin to guess at how tall to make the baffles. You may end up with the skimmer section being deeper that the skimmer instructions say. That is OK, just put the skimmer on a stand. Look at the skimmer in my pic above.
Hope this helps,