ed, i am sorry to say that a pipey high revving mx bike like a cr125 will need more than a heavier flywheel weight to turn it into a xr250 trail bike. generally the weights tame down a stronger engine, they work well on 250s for example and make them nice and linear and tractable. the cr125 is weak engine wise, so it might kill that last bit of power the bike has got...it wont add bottom, but it might take top.
generally, tweaking ignitions has little effect on power also.
instead, this weekend i think you should forget the trails and bring the lad out to REM!:) its the first week we are racing that big hill.