Lathe Spindle Orient after the deceleration

Hello, 

I am trying to obtain the original siemens behavior for my weiler lathe. When I stop the spindle after it decelerates to a specific speed, lets say 100 rpm, I want to orient it at a specifc angle so that when I want to open the chuck, I always have the pinion marked with zero at a specific position.
My lathe has a gearbox with 2 speeds and a spindle encoder that is 1:1 with the spindle shaft. Tested threading and it works so I think this proves that the encoder index pulse is received correctly. 
I have two pid loops, one for speed, one for orientation, and I switch between those two.
At this moment I cannot get the M19 to work properly, so linuxcnc gives me a "Wait for orient complete: Timed Out" 
This is the command that I try to run m19 r46 q5 p0. The spindle spins a few turns, but is-oriented never gets to be true.

You can find below the hal file for the spindle that I am using.
Before I get to the complicated part on how to start the spindle orient at a specific deceleration speed, first I think I would need to have the orientation working at least the standard way.

Thanks in advance!