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I am not sure what you are calling gunk but if this gunk is black it is engine oil. The tractor and the engine was built by Yanmar. The injection pump is lubricated with oil pressure from the engine. The seals in the pump will leak and engine oil will get in the fuel system and contaminate the diesel fuel and plug the fuel. Seals will have to be replaced in the injection pump to correct the gunk.
John Deere mowers, for the most part, use hydrostatic transmissions. These use an oil of some type (they vary by model) in the transaxle to provide hydraulic pressure to move the tractor. Older tractors will eventually experience some oil leakage over time due to seal wear. If the level gets too low, then you fail to move. Check the oil level in the transaxle. The location of the reservoir varies from model to model. If it is low, after determining the correct oil to use, fill to proper level. Then, start the tractor and work the hydrostatic drive lever forward and backward slowly and continuously until you get full speed operations in both forward and reverse. This can take a few minutes until all the air has been purged from the system.
sorry but its going to be a big job. you need to remove the gearbox to open up and get to the seals. you could try and use an additive in the gear box, its like oil seal for engine you can get it for engines gear boxes and difs and power steering. it sometimes goes by seek and seal, in older vehicles its quite good. you will need to replace the oil it will need to be done twice to clean it all out so it can get a good seal.. i.e change oil run engine get the gearbox to move for 20 min then change the oil as its warm not hot so let it cool down for 10-20 min then drain. put the seek and seal in and top up with oil and run as normal, check after a few days to see if its worked. usual does.
To check trans/diff oil, depending on how old the unit is, a good many of those type are sealed units and you cannot check or add oil to them. Again this depends on the year and model. Check with a John Deere dealer and they'll be able to tell you for sure. Matt