Motorcycle Repair: big twin clutch, clutch lever, evolution model

Question
in the process of replacing my clutch hub , 98 flht twin cam, when i put my clutch back in , it wasn't in 3rd gear, also the shaft came out with the hub , i may have inadvertently shifted the bike with the rod out now the clutch lever won't pull in, any help would be greatly appreciated ..thanks   Dave-O

Answer
I'm having problems tring to figure out how to help you. First off I don't think Harley made a twin cam in 98, are you sure its not an evolution model? The only model I know of that is concerned about gear placement is a sportster model and that is only for shifter adjustment done upon reassembly. Could you attach some photos?