So, may have it sorted...(touchwood!!) Replaced the flexible hose and bled the system, problem was still there, re-tightened all the joints on the hydraulic system bled it again and everything seems ok. Woo hoo!
Looking back at the whole thing I think there were several problems. The slave cylinder was wet inside so, by my understanding that was leaking fluid and or letting in air. The flexible was in poor condition which may or may not have been letting in air and it's possible also that the joints may have been allowing air ingress as well. That would explain why when we would bleed the system and everything would be fine, then half an hour later the problem would return.it would also explain why the hydraulic fluid was frothy at certain points during this process.
So while I may have annoyingly changed the gearbox for no reason I have at least put in in something with less miles on it and changed the gearbox oil at the same time.
I would say to anybody with similar problems to check the hydraulics first as they are at least the cheapest parts ( and easiest) to replace, then move on to the transmission itself from there. Ie; checking the shifter linkage, before moving onto to clutch and gearbox etc.
Many many thanks for you guys for all your your help, really appreciate it, thanks to David Ashcroft Ashcroft transmissions for his patience and invaluable advice, and thanks most of all to my mate Dave for helping me finally get this problem sorted. Hope this thread helps out somebody at a later date.
Rebz, best of luck with yours please let us know how you get on...