Hi I'm new to the forum. I have a 1989 lt250r that I brought as a non runner to to bottom end gone for £200. I rebuilt the engine with new seals and bearings with making sure all mating surfaces of the engine were spotless before re assemble. I changes the oil seal in the water pump and the two washers and is all back together now but it keeps loosing water slowly into the engine oil. I thought it may have been the coolant port not sealing between the clutch cover so I took it back off cleaned and used a new gasket with high quality gasket sealant either side but still doing it. Would this be just the water pump causing this or how likely is there a leak to be anywhere else.

X2 on the head gasket. I had a hard time with my 87 250 and keeping head gaskets together.

O-Ring it!!

Is the weep hole under the water pump plugged?

yep check weep hole, and use a cometic gasket and make sure gasket area is clean before you put any sealant on it.
you might have to get head gasket area cut for a flat surface. very easy fix. i would just try to reseal head gasket first.

Even though you rebuilt the water pump, it still sounds like your getting some kind of leakage.  I would try pressure testing the cooling system and see if your getting any pressure coming out of the tranny vent tube next. Dont exceed the pressure that the cap is rated for.

My parts turned up today can anyone tell me what way the oil seal goes in. I want to make sure I get it 100% right

All installed and no more leaking coolant. Happy days.