Your John Deere 790 was actually manufactured for Deere by Yanmar in Japan. The engine is the Yanmar 3TNE84EJK.
As for the metal clunking noise, you will need to clean the hydraulic filter that is located around the PTO shaft area of the tractor. Ususally it sits behind a tri-bolted cover plate. Pull the tri-bolted hydraulic cover plate, remove the filter with o-ring seal and clean it. The filter has an olefin membrane sealed sheet wrapped around the cylinder structure. Using a tooth-brush and cleaning fluid (gunk motor flush) will get the gunk off. The gunk could look bad like a mud wasp lived in there for years. Do not back flush these filters, it will ruin the olefin membrane making the filter useless.
When you open the tri-bolted cover plate, be sure to have a 10-quart clean bucket there for the fluid to drain into. To replace the fluid, you can use a fine metal screen filter on the old fluid or buy new $$$$ fluid.
Hope this helps. Enjoy your Yanmar painted green John Deere. They are very durable and last a long time. Just keep the air filter and radiator clean to prevent any over heating.
And if you ever needs parts without paying Deere green prices, the Yanmar aftermarket top suppliers are Hoyes Equipment (TX) and Fredricks Tractor Importers (AL with a dealer network.)