Sir You MUST change the input shaft seal on the main gearcase too when you have the two split for drive coupling and engine rear mainseal change. I had a problem with the seal on input shaft of gearcase in my early 9600 and the hydraulic oil wiped out the couplers rubber compound from oil saturation. As of 2002 deere did not have an updated seal for the gearcase and when I removed the old one it was evident that heat transfer inside the bell housing from the engine caused the seal to become brittle and crack. It was a huge headache until I had a chance to fix it and when I did I did as well change the engine rear main seal. Hydraulic oil was coming into the engine crankcase and showing overfull after about a week of running. When pulling the manual crank plug and timing pin plug next to the oil pressure sender I found the problem quickly when Hydraulic oil ran out the holes from inside the bell housing, then I knew where the gearcase oil was going as well.
As far as the smoke? Make sure all the filters are new NOT CLEAN BUT NEW, inner and outer air filters, fuel filter, tank screen, sediment bowl. Also some other things in question,,,, is the fuel fresh? Is the engine oil Fresh? If you smell a raw or unburnt rich fuel smell when engine is at idle then your injector opening pressures are too low due to wear and need to be tested, rebuilt, or pressures reset. I would also get ahold of enough SEA FOAM brand injector cleaner and run it through a complete tank at recommended strength to help clean up the injection pump internals, especially at that stage in the engines life. May want to think about running the valves too. What kind of OIl do you run in the hydraulics and engine? Good luck and let me know if ive just confused you further.
As far as the smoke? Make sure all the filters are new NOT CLEAN BUT NEW, inner and outer air filters, fuel filter, tank screen, sediment bowl. Also some other things in question,,,, is the fuel fresh? Is the engine oil Fresh? If you smell a raw or unburnt rich fuel smell when engine is at idle then your injector opening pressures are too low due to wear and need to be tested, rebuilt, or pressures reset. I would also get ahold of enough SEA FOAM brand injector cleaner and run it through a complete tank at recommended strength to help clean up the injection pump internals, especially at that stage in the engines life. May want to think about running the valves too. What kind of OIl do you run in the hydraulics and engine? Good luck and let me know if ive just confused you further.