I have a 2001 FXDWG and I had to replace the fifth gear seal. To do this I had to make a puller to remove a sleeve on the main shaft to get to the seal. The tool worked great however After I installed the seal I used a piece of tubing and a mallet to put the sleeve back and it seams to have pushed the whole main shaft into the transmission about a quarter of an inch. I can probobly use a slide hammer to get the main shaft back to it's proper location but did I screw something up by pushing the shaft in?

 

1/4" doesn't sound like much movement but you could have done some damage; hard to say. There are three lock rings on the mainshaft that secure the gears on the mainshaft. If you dislodged one of those lock rings; bad juju. You could have bent a shift fork but more likely you pushed the trap door bearings outward and since you were banging away on the center race; that bearing should be replaced. You need a service manual and start reading before you start banging away on your bike. There are proper tools for removing and installing the inner priimary bearing race; the sleeve that you made reference to. You also should consider removing that race and installing a new one properly. If you created any rough edges on the race, it will likely damage the inner primary bearing seal when you re-install the inner primary.

Check the below images and you can see what you might have done. You can try the caveman/slide hammer approach and, if it works, go buy a Lotto ticket because you are very lucky. I would be more inclined to tear down enough to inspect all the parts that could have been damaged, replace them and put it back together properly.

 

Don't use a slide hammer. Pull the clutch actuator cover on the right side of the transmission. Take a plastic dead blow hammer and hit the nyloc nut that retains the mainshaft and you might get lucky. Once the mainshaft is back in place get that rear tire off the ground and have a friend spin it while you shift through the gears manually. If you don't get lucky pull the transmission and send it to me here at Baker and we will rebuild it.

 

When you beat on a shaft, you are putting a lot of force on the bearing that holds its running position, and also the housing that supports the bearing.

Remove the chrome cover on the right side of the transmission, and make sure the trap door is not damaged in the area of the snap ring.

1/4" seems like a lot.

For the mainshaft to move that much, it would seem that something had to give, either the bearing in the trapdoor, the snap ring, or the lip that supports the snap ring.

 

+1 I have $5 that says you bent or popped out the snap ring....not hard to do. Don't ask how I know this....