Here's a quick summary. First remember what guiding does. The guiding system captures an image and finds the (subpixel) position of a particular star it knows about (or does similar things with a set of stars). It then tries to nudge the mount so that that the next it captures an image, that star (or set of stars) will move close to some previously found "special position". The position is found in camera coordinates, i.e. an image x,y position. However, the controls it has at its disposal are (RA and DEC) motor movements. In order to do its job, the guider needs to know which direction in camera coordinates the RA (and DEC) motor will move the image when it "nudges them". It also needs to know how far in that direction the image will move for a given "nudge". Calibration determines the directions and the amount of movement when the motors are nudged.
Now to be more specific, the motors are nudged by pulsing them for a certain number of milliseconds. (One can also send a signal to tell the motor which whether to turn forward or reverse). So, the pulse parameter you were asking about is in milliseconds. If you look at the calibration menu after a successful calibration you will see the parameters that were estimated. Here's a screenshot from part of the guider's calibration menu on my telescope computer right now.
You can see the direction (relative to the guide camera's image) for forward movements in RA and DEC, and you can see that 65.9ms of an RA pulse is expected to move an image 1 arcsecond -- which could be converted to pixels, since the system knows the arcseconds/pixel given the pixel size and focal length. These pulses for RA are on top of the constant tracking movements.
Now, in order to estimate these angles and ms/arcsecond values, the system runs a calibration procedure. It notes the initial position. It then pulses N times. In my case (see image below) it pulses the RA in the positive direction 10 times and notes how far it has gone in pixels and in what direction. (Note, it it moves more than 25 pixels, using the parameters I have, it will end early without finishing 10 steps.) That is the RA-out phase. From this movement it estimates the RA angle and ms/arcseconds. It pulses in the opposite direction to return the image to near the original position. We don't estimate anything from this RA-in phase. It then pulses the DEC motor a few times to remove backlash, and then begins an DEC-out phase, where it similarly estimates the DEC motor's RA and ms/arcsecond parameters. Again it reverses just to get back to the original position, without estimating anything in the DEC-in phase.
So, I use 10 steps, and the pulse size I use is 200ms. I've explained the RA-in and RA-out phases.
I would say calibration for me takes 2-3 minutes too. The way I do things, calibration is done rarely and its values are used frequently so it's OK to spend a bit of time getting a good calibration since it will be re-used frequently.
Note, if you rotate your guide camera after calibration, then the calibration angles will be wrong.
I am not familiar with indigo, but it is common advice to calibrate once and keep it for a while. For instance, you can probably find some PHD2 guiding tutorials online.
Best,
Hy