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Check for binding in the cardan joint. There are ears that need to be clearanced. Set parking brake put t case in neutral, hubs unlocked. Spin the front shaft you should see what i'm talking about.
I'm not sure if your front drive shaft has a blind spline or not? I'm thinking no and if you "pulled everything apart" the front u joint may not be in phase with the cardan joint. And lastly with the front lift installed the slip splines may not be engaged enough to providing proper support. It may not hurt to take it to a shop and have it balanced?
With a 6" lift your splines are probably not far enough together. If they are showing at all the shaft is extended to far. What will happen is as the shaft spins it will create a whip effect where the shaft, & yoke come together. This could cause a vibration, or humming sound.