I don't have the time to install and check your config but looking over your config I don't see anything obviously wrong with the dh parameters you came up with (although I did not check the distances of the joints).
My first suspicion would be that your graphical simulation model is not set up correctly. Make sure it reflects the rotation of Joint 1 by 90° that was needed to set up the dh-parameters as genserkins doesn't allow to set theta values. So with all joints set to zero the hand in your simulation model should be pointing to the floor. ie as in the left pose in your first picture of your initial post, joint 1 would be 0° in your config and not 90° as in the picture.
Interesting, I never quite understood how these values differ from the "HOME" offsets in the JOINT_n sections. So, are you using this to offset errors in you simulation model or on the actual robot?
