Well we took the box apart at work today, figured if it was already broke what have I got to lose, everything seemed ok, all teeth were present and it went from one gear to the next no problem at all, so it must be a little mis-alignment in my repaired gear linkage, so we fixed that again, put the box back together and it seems to go through the gears no issues (albeit on a bench) so fingers crossed that's all it was. But the clutch and pressure plate are cooked. So I thought I may aswell change the clutch and put a decent one in while I'm at it.