I have 2 904 output shafts. The front tip on one has a plain round pilot for the thrust washer, the other has some funny shaped notches with a thrust washer that has keys that engage it. I guess this it to keep the friction surface on one side of the washer only.

Whats the real difference?? I want to change the output that has the "keyed" surface with the one with the regular pilot. Any reason why I can't just remove the "keys" inside the thrust washer an use it???

the output shaft with the round pin takes a fiber washer and a steel shim on the forward drum if you mix and match need to make sure your endplay is good.

For some reason I'm not too keen on the fiber washer, I'd rather use metal but the shaft I am going to is has the full round pilot.

Any reason why I can't just drill out the metal washer and use it??

i never drilled one but dont see why you cant.