Not sure if you already know this, but for flanges you should always weld the entire circle, center included, onto your tube, then use a flush trim bit to cut out the interior of the flange, flush to the inside of the tube. You'll get a much better joint. A good router bit to own is a 1/4" spiral upcut flushtrim bit, available for $40 at woodcraft and cheaper on the net, but i can't think of the place right now. The spiral cut bits leave a much better edge than the straight cut bits. As long as you can find anything that's a circle the right size, you can use the flushtrim bit to reproduce the circle by taping it with double sided tape to the acrylic, then off you go. I used a CD to make the flanges for the injector housing on my first beckett skimmer.
You should use weldon #40, which is a 2 part polimerizing cement, to glue PVC parts to acrylic. This will work MUCH better than weldon #16, which is really just solvent with some acrylic resin mixed in to thicken it. It's a pain to find and to use; you have to mix it in 20-1 ratio, resin to activator, and it smells awful before it hardens. I find that an old salifert CA test kit is handy for the mixing; you use the big syringe to measure out, say 5 ml of the resin, then the really small one to measure .25ml of the activator, mix 'em up in a little cup made out of aluminum foil, and that's enough to attach a couple of PVC fittings to acrylic.
On the reactors I've made, I avoid drilling holes for fittings in the main tube; it's tough to get a perfect joint that I'm confident will last. Instead, I make a little box under the tube and glue the pump fittings to the box; this lets me glue PVC to flat acrylic with the right size hole. I almost never drill holes larger than 1/4" in acrylic, I just find something to use as a template, like the inside of a PVC fitting, tape it on and flush trim around the inside.
Spazz is totally right about using 3/8" or even 1/2" cast for the flanges; it will work way better. I'd go one step further and recommend either Spartech polycast or Cyro GP; it costs more than the imported stuff, but it has much more reliable welding properties. Once I made a reactor out of cheap cast where all the box joints looked great, but after filling it up there were a few pin hole leaks; what a PITA. You can avoid tapping the acrylic by using nylon wing nuts and thumbscrews; i like this alot better because you can really crank down on them if you need to, and if they break, you just get another one out of the bag, where if you strip or mess up the threads in the acrylic, you're sunk on that one.
Have fun working with acrylic, you're doing great so far!