You can go dual 2.5" or single 3". If you're planning a lot of modifications (which I wouldn't recommend on a vert), go with the dual 2.5", but if it's going to remain fairly stock, try a single 3". The duals will open up better for future mods, but will hurt your low end torque (especially with all the extra weight of the top frame and motor, not to mention subframe support on the vert). The 3" will provide plenty of power increase for a stock to fairly mild build while allowing enough backpressure to keep the low end torque in place.
DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3". DO NOT GO DUAL 3".
Get the point?
The same thing goes for the X/H pipes. The X-pipe will provide a better scavenging effect for high end performance, while the H-pipe will work better for the low end used in daily driving. If I was to build your exhaust system...
For a mild build (no more than intakes, exhaust, and tuning):
3" custom Y-pipe exhaust
Summit 3" free-flow catalytic converter
3" chambered muffler
For a more moderate build (cylinder head upgrade or more):
Shorty or Full length headers
Dual 2.5" H-pipe with catalytic converters (matched to headers)
2.5" chambered mufflers
For radical (because I know you're curious):
Long tube headers
Dual 2.5" offroad X-pipe (no cats)
2.5" straight-through mufflers
I WOULD NOT AT ALL RECOMMEND THE RADICAL SET-UP. It would only sound appropriate on a blown car. It would be very loud and not at all comfortable for daily driving, not to mention the lack of low end torque unless you have serious mods.
Good luck and let us know how it goes.