I consulted Ah Choy which is very experience with rotary engine........ Changing the transmission requires to change the engine as well...... here are reasons given.....
1)RX8 is electronically sensitive, when you change to manual ecu, you can't use your current key becos the immobiliser setting is different.....
2)As i mentioned be4, manual and auto engine is totally different, which means manual ecu cannot run auto engine and vice versa.......
3)Manual crankshaft is different from auto, if you forcefully use it, clutch bearing will damaged and the engine power loss is imminent, worst come to worst you damaged the engine and transmission together.....
As you see this not as easy as you imagine, new car are more advanced than ever, with ecu steping in the way, mod will be very difficult in the future....