Carlos;

If your overflow boxes are only 5" by 5" you might as well forget 1.5" bulkheads in them. Also, I'm not sure how you're going to get a standpipe in such small overflows, but there's probably a way. I think you want the modified durso or stockman pipes. You can do a search for these designs; you make them yourself out of PVC.

Still, you really have to deal with the holes in the bottom of your tank that are outside the overflow boxes. That's a very dangerous scenario IMO. Maybe you can put bulkheads with plugs in them, but I'd look into the idea of covering them with glass plates siliconed in place, on both sides of the tank bottom. I don't know, maybe that's a bad idea, but I'd think about it and ask some people that make tanks. If it were acrylic, I would definitely patch over the holes with acrylic, cemented in place with weldon #40. If the return holes are near the boxes, like just outside them, you could deal with the whole situation by building (or have Dan do it) larger overflow boxes so that all the holes in the bottom of the tank are contained within these boxes. Building the corner boxes and installing them is not such a big deal.

As far as the hole sizes go, definitely don't take my word for it; measure what you have, and buy the bulkheads you want before drilling anything. The size hole needed is on the label stuck to the bulkhead usually. I bet you have 3/4" bulkheads for the returns; 1/2" is really small and typically not used for large tanks.

Now, for your pump, almost any internal pump will transfer more heat to your tank than an external, which are air-cooled. The quiet one that you have is an unusually hot external, kind of like the velocity pumps. Why do you need a submersible pump for your new set-up? You could get a nice iwaki or pan world; this would be much more reliable than any submersible and run cooler.

good luck Carlos!