Thank you for that! I did some rewiring last months so it's still fresh in my head. The six button Mega Drive controllers are a bit more complicated since they seem to use the timing of the Select signal to read the X, Y and Z buttons. I can't find the link to that article right now...
In fact, I bought an AVR programmer and some AVRs not long ago. With this I should be able to read all the buttons from a 6 button Mega Drive controller. And if I add some switches on the converter I can remap buttons and such. I think this project is more realistic than the 2MB chip RAM mod I asked about in another thread.
The ADoom.readme from ADoom on Aminet directs to swap lines 5 and 7 and put a 470 ohm resistor between them (pins 5 and 7) for both 3 and 6 button Genesis controllers. The ADoom source should have Joe Fenton's code to read a 6 (or 3) button Genesis controller then. I believe the 3 button support is the same as described in the Hired Guns manual as well. It would be nice if we all used the same standards and were compatible

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