Only using ground fill on RF portion of PCB
No! Do not do that! Do the OPPOSITE of that! Very nice job with the RF section and via stitching, but ultimately you've gotta give the same priveledge of a ground plane to your FPGA. Especially for product compliance, the noise generated from the high speed signals will waste a $5000 EMI compliance test. By using a huge ground plane and a PCB stackup with thinner spacing between layer top and inner 1, you create parasitic capacitances that look like dead shorts to the high frequency, GHz components of the fast edges of your otherwise slow, X00MHz signal.
But worse yet, these edges may get to your RF section through your good idea of an unbroken ground plane in the inner layers. What would be better is to isolate the AC components between your ground planes. Break the inner layer along the interface of the RF and digital domains (really good design separating them!) And in order to connect them, use an inductor between the planes to only pass DC.
It's also a good idea to isolate your signal ground from your chassis ground, by turning those mounting holes to unconnected nets. Also don't forget to use the appropriate trace width characteristic impedance calculator for your situation, adding that ground to your RF has given you a coplanar waveguide with ground plane which first of all shouldn't have an inner copper fill (I'm not sure if you implied it did in the RF, too) Because the spacing would be so close so as to shunt all high frequency to ground. Also, be sure that you leave soldermask on your transmission lines, and don't have them as plated pads. ESPECIALLY WHEN DOING ENIG surface finish, holy moly that's a fast way to get disappointed. First of all, the lifetime of the product will experience oxidation which will change the conductivity, thickness, mu, epsilon, basically all your properties will change with oxidation. With ENIG, consider that they needed to apply a nickel layer between the copper and the gold to match the CTE's and lattice constants to get them to stick. Nickel is ferromagnetic, so you'll get attenuation above a few GHz, which could be a good thing, but will ultimately introduce non-linearity into your system which could be unintended.
I hope some of that made sense, and if not, ask me to clarify! Sorry about the giant run on sentence!