I just changed the motor on my long tail and went from a 5 to a 16 so I had to re make the motor basically. All my shafts looked to be lined up really good. (Way better than some home mades I seen) and it works perfect but my top bushing is getting hot. Is this normal? It has grease. Bc I pumped more in it while it was running but it was oozing out of the sides so its full. Any help?

And after about 15 minutes of running just now the whole shaft housing is pretty warm

More than likely your driveshaft isn't perfectly lined up inside the bushings/bearings.

Move the engine back to raise the shaft in the top bearing/bushing. Foward to lower it and of course left or right to center it. Also grease, grease and grease. Grease it every time you take it out

See that's the thing. It looks as if it would be sitting perfect. It was a good ways off at first because I was running it and the top bushing started to smoke. I realinged it and its not smoking or anything just gets kinda hot. And like I saif I ran it for a long time after the post and the whole housing was warm. Also the grease was leaking out the prop side for a lil while like if it had too mich in there. It leaked ot for a lil bit then stopped.

Check the top bushung. You may have toasted it if it was smoking. If it got hot enough to leak grease out of the lower end you heated it up pretty good. I'd think about replacing bushing and seals. Also pull your shaft and check it for being bent or bad spots