Yeah it truly is unique to every setup. I noticed I made a mistake in my post above, I said 50MHz to 2.2MHz, that should be 2.2GHz :). I think an SDR would be good enough to analyse the noise floors and RF output of all of the components for both of my frequencies in use, from there I guess I will have to look for problems then work on fixing them! I am thinking good filtering caps on power and toroids should be sufficient to keep EMI away?
I will also use my DSO Nano to look at any potential issues in power rails too, though I doubt it is going to show me anything high frequency though.