Rendering Equation for photons carrying flux
It'd be hell a lot easier if this were on graphicsexchange, since I can't use latex here but anyways.

In the first pass of Photon Mapping you don't need to use the Flux form of rendering equation. You just divide the original flux coming from the light source among the N photons, then for each photon you use Russian Roulette to determine whether it reflects, transmits or gets absorbed and store the incoming flux.

In the second pass you need to find radiance but you have information in Flux form. The rendering equation can be simply transformed. 





So all you need to do is divide the flux stored for each photon by the area. Note that the Area is often denoted as A= pi r^2 Since we are concerned with a hemisphere and the underlying area is just a circle.

About your 2nd point, I don't think the BRDF needs to be re-normalized or whatsoever since the equation is essentially the same. Note that the second term in the last equation is still a radiance written in flux form. (BRDF has units of inverse solid angle thus making the whole term radiance).