If the GWizard and Kennametal calculators are correct, there should only be about 14.5 lbs of force on the tool, the workpiece, and the router with a 1/4" tool. Based on the specs., that would cause up to an additional 0.025" of cutting error with a Stepcraft D840 CNC router. Doesn’t that swamp out the 0.0004" of tool deflection (0.0005" with 1.5" stickout) that GWizard predicts?
A 1/4 inch tool at 1.25 hp spinning at 25000 RPM can only produce 25 lbf. So even if the router was capable of that (it’s likely not), the Shapeoko3 should be able to handle it (albeit with unknown accuracy) when feeding in the X direction. (At 62 lbf, 10000 RPM at 1.25 hp would exceed the reported 38 lbf capability of the Y Axis.)
Where can I find out more about the Shapeoko modifications you’ve made?