I notcied tonight upon replacing my main shaft that one end is longer than the other...for the MX 400 pro. Which way should it go?

Looking at mine (assembled) it looks like the long end goes up. I haven't had it apart for a while. What you should look for is that, with the main gear on the bottom, the collar rides in the machined groove and the two can clamp together against the bearings. If you start to put it in backwards it's obvious because the gear and collar won't be close enough together and the mainshaft will slide up and down.