You told me about the Si5351 module before, I had forgotten that until you pointed it out. In looking up the module information I found that it has the pull-up resistors (10k) on the module. You would not want to put another set of resistor pull-ups.
You should not need pull-up resistors for the Nextion data lines. The resistor that I was trying to describe is in the 5volt power lead from your board to the Nextion display. On the v4 and v5 HFSignals boards, the Nextion was noisy when the dimmer was adjusted below 95%, This is due to the PWM power reduction used to dime the backlight on the Nextion. The 10-22 ohm resistor with the bypass capacitors kept the noise from back-feeding into the radio. That resistor will also dim the Nextion display.
I will go back and look at the schematics you provided again. By chance do you have the board layout to see if there might be something with how the board traces are run and where things are placed.