If that is the case then your encoders are 250CPR and thus 1000 pulses per rev.
Hood

I checked my Viper 100 Drivers:

The only thing to "electronic" gearing i found on the drive is the step multiplier.

The options are:
1. Programmable multiplier
2. 4x
3. 6x
4. 10x

I selected the first one, by not using any jumper on the pins. I thought this was suppose to be a 1x, but doesn't actually state if it is or isn't..

I bought all of them from U.S. Digital directly. They all came sealed in the bags and cases that read 1000CPR.

Even the product number i double checked on there website just now: E6-1000-250-I-D-E-D-B (1000cpr, .250 shaft, options I-D-E-D-B-)

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

Not sure how US Digital marks their encoders, maybe the 1000 is pulses per rev rather than the line count?
Hood

Actually hang fire on my calcs, I will think about this before I type, its always a good idea to do that, just I often dont 
Hood

Ok so start with Z, to calc properly we know 1000 pulses per rev of encoder so 1 rev rotates your screw 0.1inch as we know its 0.1 pitch so steps needed to move 1 inch  by calculating would be 10 times 1000 = 10,000
You have 10,040.73425  so divide by 1000 and that would mean 10.04073425 turns per inch so divide 1 inch by that and you get the pitch working out at 0.09959 which is close. Best using the calculated value though unless your screw is not precision.
Hood

Your new calcs look dead on. The Z pitch is .1" for sure. I'm 99% sure the X axis is 1" (i bought it new from mcmaster, just lost the paper work but swear its 1")  and the Y axis seems to be 1.25" last time i tried to get a caliper in where its housed.

The US digital site has now confused me further. In one sentence they say " we offer 256 to 10,000 pulses per revoultion (PPR) ". But on the drop down menu when you actually select the count it clearly states 1000 CPR. The ones i have are 1000CPR, what the heck is the difference between CPR and PPR.

http://usdigital.com/products/encoders/incremental/rotary/kit/e6

http://usdigital.com/assets/general/90_e6_datasheet_1.pdf

So X we start on now
1000 pulses  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 = 3.1329inch per rev that the axis moves per rev so divide by Pi and you have the dia which is 0.9977 inchr.

Hood

It is possible my leadscrew is not perfect, or it could be that my dial indicator is not perfect either. I will use the auto calculator either way. I need a better dial indicator!! Mine reads .0005" but its a cheap digital 0-1" one from harbor freight ($35USD). It seemed to work well but i would feel better with an expensive indicator.

Now Y

1000 pulses  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
2492.704346 steps are needed to move 1 inch so 10,000/2492.704346 = 4.0133inch per rev that the axis moves per rev so divide by Pi and you have the dia which is 1.278 inch