A dual 2.0" system is probably the best size for stock power when no other mods will be done but at 2 inch, you really need mandrel pipes to make the most out of it. 2.25" you MAY lose a tiny bit down low but not much and this size has been sort of the sweet spot if your planning on headers or any other mods in the future. Throw a Lextreme torque convertor in there and you wont be able to tell the difference down low.
I would keep the front cats and the entire front Y section in tact. Cut 2-3" after the 2 primary pipes have merged together. Its a small Y pipe but and a few members have tried improving on and always lost power. Most of this info was discovered by forum member JBrady so I gotta give credit hehe. Since you want the most power overall, I would forget the X pipe because you already have a balance pipe installed and removing it will guarantee a power drop. What you could do is completely mimic the stock exhaust layout and replace the second Y pipe with a much more efficient design. If your looking for the best of the best, go with a Burns Stainless Y pipe with a 2.5" IN and 2.25" out. This means a straight 2.5" pipe in between the Y pipes. Or 2.35" IN or 2.0'' for the smaller ID. Using mandrel bends will ensure the most gains out of your setup and will preserve throttle response.
I run an X pipe, 2 magnaflows and with my cats deleted I managed to drop a solid 40 pounds from the system. I run cat-less and X-pipe because i have forced induction but if I did not, the stock Y section and cats would still be in there.
Since you said your already sinning a single exit exhaust, you would have to start over. On the topic of Cats, leave them! Stock Lexus cats are already high flow metal substrate so there might be like 2hp gain at redline. The real problem with taking them off is reversion, and leaving them in place preserves the low end torque and mid range throttle response. As Jbrady puts it, they act as 1-way check valves for exhaust pulses.