Do you mean that the skeg and the main body are mismatched? This is not a recommended situation but many people have made it work.
Do you know where the leak is? A pressure test might be worthwhile.
f it were mine I would lap the mating surfaces on a surface plate or something really flat. But not too much or the bearing/seal bores will cease to be round.
Inspect everything very carefully for dings.
Use sealant goop per instructions, plus possibly more if you have gaps.
Could be the shift rod seal or prop shaft seal, thus the pressure test.