PowerPC no longer clears its own IRQ line; it is now cleared by the IRQ controller when there are no more pending interrupts. Not all games clear DMA interrupts so it was necessary to tweak the 53C810 SCSI controller and the Real3D DMA interface to only fire interrupts if a certain register is correctly set. 53C810 has the documented DIEN (DMA Interrupt Enable) register; Real3D DMA seems to use the low bit of the dmaConfig register.
Also I removed the net IRQ as no games seem to actually use it.