No question posted on my birthday deserves to go permanently unanswered. Whether it is perverse or inverse, though, I shall address your third (and un-numbered question) first. Yes. You have been rumbled. Trying to get us to believe that you were asking two questions when there were really three.
It is necessary to understand that CUDA ad PMU switches are different beasts and that they are used differently, albeit for similar ends. Both have the ability to reset the MLB completely, either because a Mac will not start up or has forgotten what its state is, or to signal to the board that the installed hardware has changed.
The MLB should be reset before anything else when the Mac fails to power-up. With the exception of the PCI Graphics, the G4 towers have a PMU, which is not the same as a CUDA. The PMU button must not be pressed more than once, and it must not be pressed for more than a second. Doing it the correct way initiates a sequence of events, in contrast with a CUDA switch which beavers away for as long as the switch is held in.
The PMU is a computer-within-the-computer, with its own memory, software, firmware, I/O, two crystals and a CPU. It is also extremely sensitive to static electricity. If the PMU is not enabled to function correctly, ie it is crashed by more than one press or a bouncing switch (which it interprets as a second press of the switch), it will go into hysterics, one result of which is to flatten your battery in 24-48hr, and another is to need a complete reset of the MLB again.
And further, when you replace the battery (which must show between 3.3 and 3.7V) after an MLB reset, you must wait at least 10sec before you press the PMU switch. Your problems, which could be thought to be extreme, may lie in a strange oversensitivity of the PMU. If that is so, do a thorough reset of the MLB: switch off the AC power at the wall (or power-brick) but leave the grounded mains cable plugged-in at both ends; remove the battery; let the Mac stand thus for 10 or more minutes; re-install the battery; unplug the mains cable at the Mac end; wait a further 10sec; press the PMU switch once only for 1sec; reattach the mains cable to the Mac; switch on mains power again; and then start up the Mac. This process should let the MLB make and remember its census of the Mac's hardware. If you change that hardware again, at the very least you should reset the PMU immediately before closing the case, and you may have to reset the MLB first if resetting the PMU is not effective.
As to your first question, ATA and SCSI buses can coexist in a Mac if they are set up correctly. SCSI is the interloper in this case, and you may need special software to support the card. The ATA version supported by the board is usually stencilled onto the MLB near each connector. The ATA bus will run at the speed of the drive if that is lower than the bus speed. Make sure that you use 'Cable Select' if the ATA bus and the drive call for that kind of jumpering.
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