Baker, I have a true dual exhaust setup on my truck. I'm running 2.5" pipes all the way. I had the Y- pipe removed and then both pipes run to a single muffler (DI/DO). I then have 2 pipes coming out the passenger side.
Yes, you can run 2 mufflers, but I would recommend having some sort of cross over pipe before the mufflers to help equalize the exhaust flows. It is preferable to use an X-Pipe as this helps to scavenge exhaust from the tube that is not flowing at that moment (keep in mind that only 1 cylinder is exhausting at any given time), so, you can create a slight vacuum at the exhaust valve so as it opens, it will be that much larger of a differential and help pull the exhaust out that much faster. Less exhaust left over, the more fresh air that can be pushed in, therefore more power. Will the truck run without a cross over pipe or an H-Pipe. Of course. But, for the little bit extra in dollars, you can get a bit more power.
As for removing the cats, this is a double edge sword. The big trick is keeping atleast some sort of cat between the two O2 sensors. The computer is looking for a different in exhaust gas levels between the two sensors. So, as long as the remaining cat is doing its job adequately, it won't be an issue. The other thing to consider is whether your area is doing emissions testing or not. If they aren't, then you are good. But, if they are, you have to make sure that the installed cat is working pretty good or the vehicle can fail the emmissions testing due to the cat not converting enough of the gases.
so, the answer isn't a black and white yes/no answer. There is some situational things that need to be considered.
sorry panda. 
