Wireshark captures different on two computers from the same port

Alright, I figured it out. It was my network adapter on wlan1. It must be something with the chipset or driver.

What I did was enable monitor mode on wlan0 and connected normally with wlan1. After that, I configured wireshark to monitor traffic on the wlan0 interface. I could see all of the traffic after that.

Assuming that you are able to utilize the network link up to 100%, the maximum network speed is NOT 1Gbps. It's less due to inter frame gaps and checksums. This is even before you start taking into account packet headers (as you correctly mentioned in your original question).

Also as implied by a comment above, a typical machine will struggle to generate packets at wirespeed, let alone generate AND capture packets at the same time at wirespeed. The one method I use to generate packets at wirespeed (on a linux machine) is crafting 1500 bytes packets and using tcpreplay. Using this method, I can get very close to wirespeed, but this utilizes the CPU ~100%, unless you are on a very very fast machine.

Having said all that, there's nothing wrong with your plan to determine the amount of data sent to TCP port 6000 by capturing and viewing with wireshark. (Make sure you ONLY capture TCP port 6000, rather than all packets on the interface.) You just need to ensure that the CPU is not loaded 100% such that the packet capture isn't able to process all packets. But then, this is true regardless of which method you use.