Thanks for your reply johnwasser!
Yes, by commenting out the attachInterrupt, the stepper still lags. Also, by commenting out all the Serial.print in the for-loop, it does not lag.
However, by rotating without any Serial-print except at start, midway(rotated 360 one way), and at the end, the pos-variable is printed differently everytime, but for instance now [0,549,-844]. It is supposed to be [0,1000,0], (start,360,back), of which our result makes no sense.
A remarkable problem is also that it heats up, after a couple of go's it is really hot.
Any idea how to measure real position, working around this problem?