There's got to be a bazillion ways to insure they're straight. Assuming a straight hinge line I'd do it by making sure they were square to the hinge line (or offset by my desired amount), then making sure the stab is square on the fuse by the usual triangular measurements (you do make sure of this, don't you?). If for some reason there isn't a straight hinge line, I'd draw a reference line and make sure they were square to that and proceed as above.
Speaking as an engineer with a long-time interest in aerodynamics, I can authoritatively quote numerous folks who actually know this stuff and say that yes, absolutely, it does make a difference. Just like end plates on a wing, or winglets, they will slightly increase the effectiveness of the stab/elevator as a lifting system, and done right they will reduce the induced drag.
Speaking as an engineer with a long time to develop cynicism about nearly everything, I can also opine that whether they make enough difference to matter is a matter of conjecture, and whether the difference is positive is a matter of getting the details right. While the induced drag at high elevator deflection will almost certainly be lowered, the interference drag from the extra surface intersections will be higher. Further, when you have movable surfaces working against end plates like this, the necessary gap width to gain any advantage can be incredibly small; make it too big and you don't get much improvement in induced drag, you lose your extra lift, and the interference drag goes way up.
History tells all, and history tells that a lot of planes have been successful without them, and a lot of planes have been successful with them. I think whether you use them really falls to aesthetics and personal preference.