(1) As your hinge is defined along the global y axis, there is a need to define the bending stiffness along the global y-axis, which is the x-axis in the hinge local joint axis. Your definition is correct.
(2) It is up to you to make this gap to be smaller or not. It may affect the accuracy of the results, as there is no “gap” between the two parts of the original flexible structure.
(3) It is great if there were no such surfaces.
(4) T1 (Part1) at (0.0, 0.0, 1.0) and T2 (Part 2) at (0.0, 0.0, 1.0) will be fine, and the hinge axis is along global y-direction. It could be better to let the joint's vertical location be on the bending neutral axis.
(5) please check the masses and moments of ineria of the two parts are defined properly.
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