After the header, a good size would be 2.5 inches. 3 inches is a little large and will kill exhaust velocity and your low end torque. 2 inch is a little small, your EGT's will be a little higher (because of the restriction), but you will produce better low end power, while sacrificing your top end.
I would reccomend going with a dynomax ultraflow or magnaflow brand mufflers (or anything using a perforated core [louvered is acceptable, but the louvers themselves make the air turbulent, which restrict air flow.])
The Dynomax superturbo mufflers (aka "phat-boy") flow ok and are queiter. I would not reccomend going with any flowmaster, they are restictive for their size. My buddy Jim Ratto ran some tests on his 2276cc engine by using the same header (1 3/4" primary) and changing only the exhaust, he said that the magnaflow 2.5 inch muffler produced more power, while having 20 degree lower cylinder head and oil temps than a 3 inch flowmaster.
Everyone wants madrel bent this and that to straighten out the flow of the exhaust, why would you want a muffler that makes the exhaust split up and go all over the place? Totally defeats the purpose.
This is a picture of a flowmaster, see all the baffles that are in the direct path of the exhaust? not good for flow.
compare to magnaflow
Hope this helps.