I wouldn't have wiring in between cards like that unless you can help it. Better solution would be to have the PWM connector on the card go around the back where the converter is hidden, then the fan wiring gets hooked up to it there.
If the PWM converter PCB doesn't have a heatsink it might fit ok but it would run a touch on the warm side but would still probably be ok for the Gelid fans. The transistor gets warm once you start adding more and more fans. I can also minimise the height by using a fan connector on a wire rather than on board like most I make. There have been several I've made with connectors off board.