I had a car accident a few months back and they had to fit a new condensor and regas the system. Anyway at the same time I had a rat in my fan so they were unable to test it out. After getting that cleaned up I thought it was all fine.. the fan was quiet now and didn't smell like rotten dead things but I noticed the same day that when doing say any more than 20 km/h, the car would jerk slightly every few seconds. This was obviously the clutch on the compressor engaging and disengaging. At one point it even did this at idle.. and I got out of the car to hear click clack every 3 seconds.

Obviously I'm not using the aircon because I don't want to **** up the compressor. I haven't had time to get back to an air conditioning place but I took it back to the crash repairer who crapped on about my TX valve and that it was not accident related and that I would have to get it fixed myself.. riiight. So after that I was reading and found out that if the pressure levels drop in the system the compressor will switch off to save itself from being damaged.

Is it possible that the gas level is too low and that this is why the compressor engages for a few seconds.. with high pressure.. and then detects low pressure and switches off?

Yes it is gas related.
I had some (of the many times) warranty work done on my TJ sports and it involved a new compressor. After fitting i had exactly the same problem as you have just described. I took it back and they fixed it right away. I thought it was that there was too much gas in the system and they just removed some and it worked fine. I am pretty sure it is gas levels, up or down. get it back for them to check out with their pressure guages.