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I am using xnaron's carriage mounts, which are generated with an OpenSCAD script. The parameters were set at 48mm center-to-center, and that is what I measure.

My probable mistake was not verifying that the effector I printed, a modified version of the one barnett posted around here, had the same width for the arms. His effector comes out at 50mm c2c.

I'm not sure what I'll do now. I think that even with the base setup that I originally described (where it lifts between 0.008" - 0.018" at FLR) I should be good enough to throw the original hotend back on and reprint the carriage mounts with a 50mm c2c distance, matching that of the effector.

I'm almost annoyed enough to start deriving the equations of motion and putting them into a Matlab (actually Octave) script. I've been wondering if it would be possible to create a solver for which you input the measured dimensions and errors and it can converge on a solution for the required fixes to the tower positions and/or printer radius...

I'm just about to dive into similar issues. I think it'd be great if everyone printed this: http://www.thingiverse.com/thing:50505 and posted the results so we have a visual before/progress/after to go along with any changes being made. I will post mine in the next couple of days after I get it print ready again.

That is a great calibration print. Hopefully Wednesday I'll be back up and running, at which point I'll surely give it a try and post some results.

My printer is packed away due to house renos, but as soon as I get it running again I'll give it a try and report back.