I have to put a new clutch kit in my 1978 x1 9 dose the whole motor have to come out?

You can split the engine and gearbox in the car but you'll need to make sure the driveshafts detach easily as the first step. It is not unusual for the bolts on 5-speed to get stuck and rounded off. Check that first - once that's ok it is easy enough. The 1300 is a bit easier to deal with.