I hear you. I have tried various cut methods with this setup, but I have settled on cutting from underneath using a 1/16th slot cutter. Cutting from underneath, I have to shim the indexer the appropriate amount depending on which billet size (talking OD) I am making. But the benefit is I can use my cross slide and make multiple passes and clean up passes to cut whatever slot width I want. It works well considering the equipment, save for the drawback of a 1/16th minimum size. I actually just feed it manually, though I have done it under power as well.
What do you mean you reversed the tail stock? I set my indexer up on the right pointed toward the headstock because of the router mount position I built (so I can rotate my compound 90 degrees and use the same setup for threading/parting rings). Given the indexer is on the right, reversing a tailstock for support when using this setup to mill vee grooves or perhaps plunge cutting for dot inlays after part is assembled is something I want to try out.
Kelly