For the first half mile when the clutch is cold it squeaks every time I change up. It make a noise at no other time, neither does the thrust bearing(no rumbles, etc). What could this be, is it a sign that it's on it's way out?

I've since found out that it's something to do with engine movement as when I throttle on and off again in a low gear it makes the squeaking sounds. It must be exhaust related as it gets a lot quieter or completely stops after a short time when it's warmed a bit. The seal and springs on the exhaust less than a year old.
Maybe some spacers on the springs is required?

First thing i would check is all engine and gearbox mounts.

Then check all other bolts etc

Thanks for the reply. I had a quick look at the engine mountings and they all seemed tight but I'll have a closer look in a day or two.