Here is a link to the 38-44-50C series mower decks - Owners Manual.... Owners Manual

Here are the pics of my mule drive. Unfortunately I have the 46" deck instead of the 38 or 44. As you can see, I have about an inch of rod sticking past the nut. I would think the smaller decks should be similar.

I am still leaning towards your deck being mounted on the wrong hanger assembly or being installed incorrectly some other way.

Thanks for the pictures. That's what my sister's tractor look like but the rod is all the way in with the nut ready to fall off in order to adjust the tension to the first little "B" notch. I'll have to look at the mounting of the deck like your third picture shows. Another thing. Are the front pulleys supposed to angled a bit? I first thought they were bent but I noticed that the pulley on the deck is off center. So I'm guessing that that is OK.