Sam - great questions and there's huge amounts of information, ranging from relatively simple, to massively technical
However, your comments are broadly correct
On a normally aspirated car, the induction side is "tuned" - I can't remember which way it goes, but lengthening and shortening the inlet tract has a noticeable effect on performance, particularly torque. This is why the VIS was built (Variable Intake System) and also BMW's (in)famous VANOS - they both alter the inlet tract length for better tractability or power
As for the exhaust - yes, an NA needs backpressure, which creates resonances in the exhaust. This is tuned for efficiency (and noise) but serves to assist the filling of the cylinder on the intake stroke and serves to help empty the cylinder on the exhaust stroke
Turbo systems are less complex
On the intake side, its purely a matter of getting as much gas into the cylinder as possible, so its all about making the inlet free-flowing. This in itself is complex, requiring significant knowledge of fluid dynamics and flow characteristics. Simply attacking a head and making the ports bigger will probably do more damage than good.
On the exhaust side, I recall someone saying the best exhaust was no exhaust
Probably not too good for the road, but great for performance. Bring your own Nurofen! However, its simply a case of getting the gasses away from the head as quickly as possible - there's no point in trying to create tuned lengths to help with scavenging of the cylinder, as the turbo gets in the way.
I seem to recall that there can be an issue with some turbos - something to do with pressure differential either side of the exhaust turbine. This is what kills the oil seals on standard turbos, but I remember reading it can have an adverse effect on performance too.
There's plenty of mis-information on exhaust sizes, but 3" is accepted to be fine for a modestly-tuned Coupe - quite simply, there's no way that a 300bhp 2-litre Coupe lump could produce enough gas to make a 3" system restrictive.
Have a read of Guy Croft's site - lots of info there