Before editing any route file, back it up first in case it all goes horribly wrong.
To change the stopping points, open up the route file and move (best to cut and paste to prevent accidental duplication) the stop commands to wherever you want to put them, presumably in line with the S-car stop signs.
If you are not familiar with editing BVE routes, this is the sort of thing you will need to move...
53187,
.Freeobj 0;383;-6;0.3,
.Stop 0;25;25,
just the bit in bold and take care with the syntax, all commands are separated by ,.
BTW, in the example shown, you are allowed + or -25m leeway each side of the nominal stopping point; for a more challenging drive, try reducing this by altering the 25's to say 10.