Just get the acrylic at lowes. I used 1/4" and recommend that since it will hold up better under the weight of plugs and stone. I got it cheaper cause I talked them into selling some scrap that they had but it was not easy to get them to sell it, I had to go up to the store manager. I think they sell good size pieces for $33 that sould be enough for a nice size rack. The nylon rod I got here
McMaster-Carr I don't remember the size I got though. Get nuts to go along with it. The rods I got are thick but they didn't need to be. You might be able to find these local to you to avoid shipping. The place I linked is local to me. You might try grainger or even any local hardware store even.
Basically all I did was cut the the pieces to the size i was looking for. Lowes will do this for you or if you have a table saw that would work too. I layed out the hole locations with a dryerase marker. Then drilled all the holes. This was the hardest part, get a piece of plywood and lay the acrylic down on top. That will help keep the acrylic from chipping the underside. Drilling a pilot hole with a small bit will help keep the bigger bit from walking on you. I just used a regular wood bit since that what i had laying around. You have to go slow enough to not break out the hole but fast enough so that your not melting it. In hind site I may have done this in a container of some sort and had water in it to help keep things cool. After i drilled all the holes i used a scrap piece of acrylic with a flat edge to scrape all the burrs off. That way I didn't have to use sandpaper and was able to keep the clear look.
Shelves: just use the rods to hold the shelves. Use the nuts to hold it and another nust to secure it. that was really all i did for that. Just cut them to the length you want. Its really fully adjustable you just need to adjust the nuts to raise or lower.
Im sure there is a easier more effecient way of doing all these things, I built this during hurricane Sandy and was running in and out of the house to avoid dying LOL. But I think it came out rather good. I have since taken down the frag tank and have this just sitting around waiting for my next frag tank.
As for the cost, I think this cost me about $30 but I got the acrylic cheap. I'd be willing to bet though you could easily make a shelved system to fit a 40 breeder for about $50 if you don't get crazy buying special tools.