Grant - just read your story. Reminded me of when I got started in this hobby. Bought my first Cub Cadet from a JD dealer that had overhauled the engine and repainted the tractor. It was a Model 1450 with 50A deck and 42 blade. I knew absolutely nothing about these tractors. I used it about 3 months with no problems and really loved the tractor. Then one time when I was using it I thought it sounded like a rod was starting to knock. Took it into the garage so I could hear it better. At idle it didn't seem bad but as soon as I pushed the throttle up there was definitely a loud knock. I decided I better get it to the Cub Cadet dealer since I bought it without any warranty. Got it to the Cub dealer and he listened to the engine run, heard the knock, but told me not sure if it was a rod or something else. I told him to call me once he determined how much the repair would cost. I called after 2 weeks (grass was getting tall) and he hadn't had time to get to it yet. The next week he called me, said it was all repaired and total bill was $250 (don't recall exact number). He told me the 4 bolts holding the rag joint together at the drive shaft had come loose and he replaced them. I thought, $250 for 4 bolts and a rag joint. I better learn how to repair these things myself. And that's how it all started.
So, in you're situation I'd remove the side panels and try to get a good look at the front end of the driveshaft. The firewall between the gas tank and engine are kinda in the way but I think you can get your hand in there and see if it seems like anything is loose. Maybe you can crawl underneath and attempt it as well. It's a somewhat complicated joint assembly connected to the engine flywheel. I mainly suggest checking the rag joint and try to see if the bolts are loose, or anything else in the area seems sloppy.
Also, remove the center frame cover and get a good look and feel of the rear rag joint. I suppose the noise could transfer from either.
Hope this helps and let us know what you find.
Hydro Harry
Old Cubs Never Die