There were two distinct 9600 models and one 9500 model. The 9600 models are the original 9600 and the PM 9600 Enhanced, also know as the Kansas 9600.
There are three differences between the 9500 and the 9600. The power supply connector on the logic board is different (IIRC), the case is different, as others have mentioned, and the ROM has been updated from 77D.28F2 to 77D.34F2. Chips are marked 341S0168 - 341S0171 and 341S0280 - 341S0283 respectively. Otherwise the 9500 and original 9600 logic board are identical and the ROM revision provides little if any change in performance.
The difference between the 9600 and the 9600 enhanced are slight changes in the pinout of the CPU slot to support the new CPU card (more 3.3V supply?, haven't mapped it out), the L2 cache is removed from the logic board, and the ROM is once again updated to 77D.34F5. Chips are marked 341S380 through 341S383.
If you want to use an ATX case, your best option is to find a Power Computing (PCC) Power Tower Pro logic board or machine. It will fit properly in an ATX case adn use an ATX power supply without modification. Logically it is identical to a PM9500 logic board.
Another alternative is the Umax S900 logic board, but the power supply required adapting to use an ATX and the lower four slots have various issues, which are easy to deal with once you understand them, but simply make it impossible to use some combinations of PCI cards.