Problem solved. I used this instructions and the three ways are working, confirmed the wiring on the light fixtures first.
How the 3 way were wired is that the HOT/LINE is connected directly from main box to remote box, then the main switch is the red wire (black screw), white and red are the traveler and load.
By following the above wiring diagram and capped off the HOT wire between main and remote, I am able to get this to work.