Sorry had calcs arse for tit, talking on phone and typing at the same time is not my strong point

, heres the new calcs with 1000 PPR

X Axis

1000 per motor rev

Gearbox is 10:1 so motor rotates 10 times for one output rev so that is 10,000 steps per output rev

3191.931756 steps are needed to move 1 inch so 10,000/3191.931756 = 3.13289inch per rev that the axis moves per rev so divide by Pi and you have the dia which is 0.9977 inch.

Y Axis

Same encoder same gearbox so

1,000 steps per output rev

2491.704346 steps are needed to move 1 inch so 10,000/2491.704346 = 4.0133 inch per rev, divide by Pi and you get 1.278 inch

Z Axis

Same encoder so still 1000 per rev of motor, no gearing so again 1000 per rev of screw. 10,040.73425 per inch so 1000/10,040.73425 =0.0996 pitch screw

So looks like the Z at least is out as I presume you used the auto calc and your measuring was a bit out.

Hood