To be fair the marks are already there. You can always put it back again.
As N2O says it is tens of millimeters. When I did mine the act of tightening was enough to take it out. In the end I left the bolts ever so slightly loose and with a piece of wood just tapped ever so gently so it just moved then tried again. In fact in the end I did it with the engine running and a mate in the cab to turn the engine off as soon as revs went too high.
CPS is probably safer to play with though!
One problem at a time. Modulation has nothing to do with fuelling. Moving pump mid section will not change that. I want to see 45% to 55% modulation at 750 RPM first, then we can move on from that.