Well after doing research upon other forums i was able to gather lots of information with my symptoms. It was narrowed down to the inner most bearing of the unit bearing on the right hand side. This bearing is only used when the hubs are unlocked which is why it only vibrated when they were unlocked. Why there was a 2 month period where it didnt, i do not know. This bearing can be replaced fairly cheap and seperate from the unit bearing but i just installed a whole new bearing assembly.
This truck now drives much quieter and smoother. Going over bumps is smoother and not as chattery. I think i will replace the drivers side soon as well to prevent it from getting as bad as the passenger side.
Here are some pics of the old bearing and the metal shavings within the hub.
