I assume you were using the Simcraft BiS profile for your first iteration? I believe that was written before the RPPM change and stack haste may have been more viable, now that looks somewhat less likely.
I'd also suggest perhaps adding a no-expertise or partial expertise value for Renataki's because getting the full amount of expertise out of that trinket seems unlikely.
On Rune, I agree that the simple net EP approach I used above probably isn't perfect but unlike many other classes rogues don't have a lot of mechanics that allow gaming a Rune proc, mastery stacked snd as sub is the only thing I can think of, so its probably good enough.
Finally, these results do appear to basically line up with some numbers I generated about a week ago using ShadowCraft (assuming 15% haste). The big differences appear to be Rune (which Shadowcraft overvalues) and valuing bad juju over Renataki's which I can't really explain.