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There were 6 different transmissions offered with the RX-8 worldwide that I am aware of, 3 automatics and 3 manuals.
The manual transmission variants were:
This is the most common of all the transmissions, being paired with the Series1 6-port engine. It's primary weak point is 4th gear. It is sufficient for street use, however on the track 4th gear failures become much more likely. Reverse is located to the right of 6th gear, and requires pushing down on the shift knob to enable the shifter to enter the reverse gate.
This is the R15M transmission used in the 1993+ RX-8. It was only available with the RX-8 outside of North America, and was usually paired with a 4-port engine.
4th gear was reinforced to be stronger than the S1 6MT. Reverse is located to the left of 1st gear, and requires pushing down on the shift knob to enable the shifter to enter the reverse gate.
All manual transmissions are directly swappable with the other manual transmissions. There are slight wiring differences, but they are easily solved without complication.
The automatic transmission variants were:
This transmission was only available when paired with the Series1 4-port engine.
This transmission replaced the 4-speed AT above, and was paired with the 6-port engine
I am not currently aware of the difference between this transmission and the 2006-2008 6-speed AT, however this transmission has a list price that is approximately half of the other 6-speed AT, so it stands to reason that there is something significant different about them.
The Automatic Transmissions for all years had steering column mounted paddle shifters that function identially to manually telling the transmission what gear to be in when the automatic shifter is located within the "M" gate. These shifters are not indicative of a double clutch or fast shifting mechanism, it shifts just as slow as when you don't use the paddle shifters. This is also NOT "Tiptronic". That is a Porsche brand name for a transmission that you can manually shift (Porsche does let some other manufacturers use the name under license). Mazda calls it "ActiveShift". Yes, they do the same thing as far as most drivers are concerned, but there are significant differences under the skin, so calling it a "Tiptronic" is not correct.
The automatic transmissions also have a slight peak torque advantage vs the manual transmissions, but cripple the peak power because of it's inability to reliably handle the heat and fluid management of the 9,000rpm redline of the manual transmission equipped engines. This is why the automatic transmission equipped engines have a lower redline of 7,500rpm.