Hi Ryan,
interesting, It's a tough decision as a belt modded, stripped down, new bolts and tuned NEQ6 is essentially what the EQ6-R is (apart from the handle which is a simple but great addition)
Hard to say which would be the better performer without seeing actual RMS figures. I and others have been getting an RMS of around 0.8" out of the box with the EQ6-R (I won't be attempting to tune that before the warranty is up).
I'd be tempted by the tuned NEQ6 though, I suggest you try and find actual reviews of an Rother valley tuned mount and also think about what payload you are likely to use in the next few years.
There is never a straight forward decision to make in astro imaging, I will be buying a cooled camera this year, that will be a real headache to choose as well!
good luck,
Rob.