Assuming that the engine has been well maintained and is properly tuned, is it idiotic to run a street port and a T66 with the factory S5 stationary gears and apex seals?

 

No, it's perfectly fine. So long as the proper modifications are done to allow for the turbo to function properly and safely.

 

Cool, thanks. Is the main factor that effects the stock internals the RPM's that the engine sees, not necessarily the boost/power levels?

 

Argueably, yes. Of course someone is bound to come and tout the necessity for 3mm seals for high boost/BHP levels. But it's been proven that it isn't a necessity, and that high boost/BHP levels can be seen/made with even the stock mazda 2mm seals provided the motor is tuned well.