I know that automatic transmission 8's came with a 4 port engine, and the manuals a six port...but...I really don't understand even after searching what the difference between the two is.

So...besides the transmission difference, how do the motors differ?

 

The '06 and current auto RX8s have a 6-port engine too... its only the '04 and '05 auto models that have 4-port engines.

The 6-port has more HP, torque, and a higher redline.
The 4-port has two intake ports (per rotor) while the 6-port has three (Auxiliary port is the 3rd).
The 4-port doesn't have a VFAD to allow more airflow into the front duct.
The 6-port has six fuel injectors (3 per rotor) while the 4-port only has four (2 per rotor).
Might be others... that's all I can think of at the moment...

 

the ECUs are different
the 09+ engines are waaay different
the 4 port has 1 oil cooler the 6 port has 2
different drive shafts

 

4 port has 2 intake ports per rotor
6 port has 3 intake ports per rotor but the upper port opens only when needed more like a variable intake valve timing stuff to piston engine

4 port intake layout


4 port side housing


6 port intake layout


6 port side housing