I own a 650 like yours and a couple of years ago it got to running poorly and went to pulling down and then smoking some and finally quit. It needed the injection pump rebuilt. The pump as you say is almost a built in. However, do not despair. It is not too bad to remove/replace. The main thing you need to do is not to get in a hurry and also clean the area around the pump very-very good and keep it clean while dealing with the injection pump and injectors. Take the lines loose from the pump and the injector and mark them so you can get them back right. DO NOT BEND THEM!!! There are about 4 nuts holding the pump into the governor housing take them off and very carefully tap and shake the pump till it loosens and lift it out. Be sure to keep the shim pack between the governor housing and the pump intact because these set the timing. Measure the thickness of them and then buy the shim package from John Deere and use the EXACT same thickness of shims when replacing the pump. I sent my injectors as well to be check/reconditioned at the same time. They probably both need inspecting or repairing. Be sure you hold the line nuts and the fitting it tightens to when reinstalling them. Bleed everything all the way to the injector itself before trying to crank it. I installed a small electric fuel pump in the line on my tractor and also installed a furnace oil filter unit that uses a Wix # 4104 filter in addition to the regular filter with the glass bowl. I got 1250 hrs out of my pump before rebuilding it and the price for rebuilding pump and injectors was over $650.00. It has been a good dependable tractor though.
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