Latency is a function of the number of steps on the path between the source (microphone, camera) and the output (speakers, screen).
Changing clocks will have zero impact on latency.
The delays you have include:
- device internal delays - waiting for screen vsync, etc...; nothing much to be done here
- device interface delays - a shorter cable will save you some time, but nothing measureable
- software delays - your operating system and browser; you might be able to do something here, but you probably don't want to, trust that your browser maker is doing what they can
- encoding delays - a faster processor helps a little here, but the biggest concern is for things like audio, the encoder has to wait for a certain amount of audio to accumulate before it can even start encoding; by default, this is 20ms, so not much; eventually, you will be able to request shorter ptimes (what the control is called) for Opus, but it's early days yet
- decoding delays - again, a faster processor helps a little, but there's not much to be done
- jitter buffer delay - audio in particular requires a little bit of extra delay at a receiver so that any network jitter (fluctuations in the rate at which packets are delivered) doesn't cause gaps in audio; this is usually outside of your control, but that doesn't mean that it's completely impossible
- resynchronization delays - when you are playing synchronized audio and video, if one gets delayed for any reason, playback of the other might be delayed so that the two can be played out together; this should be fairly small, and is likely outside of your control
- network delays - this is where you can help, probably a lot, depending on your network configuration
You can't change the physics of the situation when it comes to the distance between two peers, but there are a lot of network characteristics that can change the actual latency:
- direct path - if, for any reason, you are using a relay server, then your latency will suffer, potentially a lot, because every packet doesn't travel directly, it takes a detour via the relay server
- size of pipe - trying to cram high resolution video down a small pipe can work, but getting big intra-frames down a tiny pipe can add some extra delays
- TCP - if UDP is disabled, falling back to TCP can have a pretty dire impact on latency, mainly due to a special exposure to packet loss, which requires retransmissions and causes subsequent packets to be delayed until the retransmission completes (this is called head of line blocking); this can also happen in certain perverse NAT scenarios, even if UDP is enabled in theory, though most likely this will result in a relay server being used
- larger network issues - maybe your peers are on different ISPs and those ISPs have poor peering arrangements, so that packets take a suboptimal route between peers; traceroute might help you identify where things are going
- congestion - maybe you have some congestion on the network; congestion tends to cause additional delay, particularly when it is caused by TCP, because TCP tends to fill up tail-drop queues in routers, forcing your packets to wait extra time; you might also be causing self-congestion if you are using data channels, the congestion control algorithm there is the same one that TCP uses by default, which is bad for real-time latency
I'm sure that's not a complete taxonomy, but this should give you a start.