The average density of the universe is about 10^-27 kg per metre cubed and the mass of proton is about 1.6 X10^-27 kg. So, as Hydrogen atoms are the most common atoms in the universe, there will be about one atom per metre cube. You could easily pick a random cubic metre of space with no matter in it.
The photon question is much harder to answer. The 'size' of a photon will relate to its wavelength and the spectrum of the residual microwave radiation which would be the very least you could expect to find is centred about the cm wavelength of microwave radiation. You could say that the lowest frequency photons (corresponding to sub - audio electromagnetic perturbations) have wavelengths of millions of km so they would seem to 'fill up' everywhere with 'something'. Remember, as the frequency of an em wave decreases, the energy of a photon is less. So there will be loads and loads of these low frequency photons everywhere - compared with the relatively few high energy X ray and gamma ray photons.
I just had a thought; Feynman discusses photons in terms of interactions between charged particles (ref. the well known Feynman diagrams).You could say, then, that for every pair of charged particles in the universe, there would be a photon because they are all affecting each other to some extent. That means the place is just chock full of the things! Far, far more photons than matter particles.