Hey Henrik,

You are thinking correctly on the absolute angle needed.
That's where the pulse counting comes in...
On the arm I've got designed in SolidWorks now has the following:

500 line encoders
2000 counts in quadrature
10.8:1 gearing
21600 quad counts per 360 degrees

Upon "zero button" press, we'll get degrees "moved" like this:

\\\\ Snip of VB Code ////
Const DPP As Double = 1.66666666666667E-02 <<< 360 / 21600
Dim DegreesNow As Double
Dim CountsNow As Integer
DegreesNow = CountsNow * DPP

If I'm thinking correctly, that will give us the degrees "traveled" by each joint.
If I am reading your question correctly, are you referring to the angles from "zero planes"? (dead vertical and dead horizontal)

Let me know if my thinking is correct?

Hard for me to keep it all straight!

I'm will also be doing the CNC machining for the arm components as well...

Too much for 1 guy to think about!

Let me know what you think.

Thanks again,
Chris