I don't think you're going to be able to fully duplicate the SNES H/V counter behavior by using what's built into MAME. There are some really odd things, like scanline 240 on non-interlace odd fields on NTSC sets missing one pixel (something to do with color burst, I've been told), and dots 323 and 327 lasting two clocks longer than the others (except on the short line mentioned above.)

Really, the PPU and CPU need to run on their own clocks, and you also have to support the bus communication delays between them, eg CPU write to a PPU reg takes 6 clocks to acknowledge, where a read takes 2 clocks to acknowledge.

Without this stuff, you won't be able to make use of most of my regression test ROMs frown
Those will save you a ton of headache with IRQ / NMI bugs.