Usually you do get to make a program to help you out and yeah going by hand is a long and tedious process which is why few ever do for a long game like this. The other options include a pointer tool like atlas (
http://www.romhacking.net/utilities/224/ ) which is almost a programming language unto itself or you make a spreadsheet.
Hopefully there is some nice indicator of an end of section (I have often seen sentence by sentence pointers and that means you can use the fullstop, what it is here I can not remember) so you dump the initial pointers into a spreadsheet, do a search for whatever end marker/start markers you have on your edited script and dump that into the same table and then adjust accordingly (the start or end markers might be a set distance from where the pointer wants to go to). Alternatively you could try actual lengths from your new script but that is almost all the way to programming your own tool.