Neil- a quick suggestion about mappers: use whatever mapper you want, but keep in mind that very very few games had 32kb of WRAM. In fact, here is a list of every single NES and Famicom game which used 32kb of WRAM:
http://bootgod.dyndns.org:7777/search.p
9+20+41+53
My guess is that an MMC5 may be your most viable bet for an "available" mapper for freeing yourself from timing constraints. However, only one game exists which used this combination of MMC5 and 32kb WRAM: Romance of the Three Kingdoms II.
As for scaling the pulses with a microcontroller, that might be a bit overkill. Perhaps a solution with a 555 would be easier to implement as a pulse multiplier.