I think you should start with sharing the schematic. It is too much work for me to bother looking at a PCB and try to figure out what traces are doing what.
The frequency signals range from 250 to 500MHz.
This isn't too high yet.
What I know and have done so far:
The lengths of traces carrying the high-frequency signals should be shorter than 1/10 of the wavelength of the highest frequency taking into account the propagation delay due to PCB.
This is a common rule of thumb, but the main thing is not that they should be shorter, rather that if they become longer, you should start taking the line impedance into account.
The traces for high-frequency signals should possibly remain straight or should have a radius of curvature.
At 500 MHz, this doesn't really matter too much.
The width of high-frequency signals should be 3mm in order to match the impedance of 50ohm for PCB of 1.6mm thickness & FR 4.6.
That is quite a wide trace. I would consider going for a 4 layer PCB for this kind of design, as routing without disturbing your return currents will be challenging at best on a 2-layer PCB. A 4 layer PCB will also reduce your 50 ohm trace width significantly and as a result make the entire routing process more manageable.
Most of the issues you talk about in your questions are minor, likely even insignificant, at 500 MHz, unless you are doing ultra-high-precision measurements or super sensitive measurements (at which point you should stop using rules of thumb anyways and switch to using electromagnetic simulators).
500 MHz has a wavelength of like 60 cm in free space, so unless your PCB is massive, and don't break your return currents, things will be fine.