I just had the same prob pulling my Johnson 4 hp apart, shaft stuck in the motor, l had this apart 18 months ago replaced the impeller and greased the spline before refitting (ironical the impeller was still OK and 22 years old, new 1 has lasted less than 2 years). The motor did has just overheated, hence why trying to pull apart now. Photo shows how l got it apart (after removing power head from housing), you need to remove the bottom bearing seal so the timber sits flush with the motor lower casing (18 mm hole thru wood and 13mm water hose over the shaft), then drive apart with some wedges. I had tried bashing it apart with the power head in place in the casing, but ended up damaging the lower end housing were the gearbox sits, but that shouldn't stop it from going. I should have done my second method in the photo first.
Photo wont load, so as above have wood slid down shaft, laying flat against the lower motor housing (put some cloth between wood and bearing so no debris goes into bearing), clamp the shaft in a vice by gripping the water hose that is slid down shaft. Leave enough room between the jaws of the vice and the block of wood to enable the wedges to be driven down either side of the shaft. Keep alternating hitting the wedges with a solid hammer , supporting the motor until the shaft comes out of the power head.
Now back to putting it together again.