As said already, the 16mm is waaaaay too large. For a dual disc 14mm is better, and I like 13 even more. Your brakes feel like crap because the leverage is wrong. As an analogy, it's like being two feet from the fulcrum of a teeter totter trying to lift the person on the other side - it would be tough to lift even your two-year-old.
It's just a matter of leverage.
And the standard rubber brake lines work just fine - until they age and collapse internally. It's true, they've got a little more flex, but you shouldn't be working your brakes that hard anyway. Fix the source of your problem, then decide whether to replace the brake lines or not. Right now, with the over-large master cylinder, stainless lines will actually give you a stiffer lever.
And to make sure it's all very clear - the LS takes the shallow disc, the standard R65 with snowflakes takes the deep dish.
Bruce - nice LS! Like those discs!