I have an 06 Ext Cab standard bed 4x4 5.3L silverado,

What diameter cat back system will bolt (not weld) right up to the rest of the stock piping? most kits are either 3" or 2.5" and i hear the stock is 2.75"

If you purchase a system, no matter what size it is it should still bolt right up. Custom exhaust is where you have to worry about sizes.

3 inch is the way to go IMO

Just about any good aftermarket exhaust system manufacturer will have a website with an application chart or something similar. Whatever you want to do, either the whole system or catback, just choose what's right for your model truck and it should bolt right up.