You should be O.K. just putting the spacer back in place, that shouldn't matter at this point. Replace the pads one at a time, don't take both of them off. Then you can measure the other side and match them. I would think the spacing would be measured from the front of the rear bow to the back of the second bow, but I don't know that for sure.
Don't over analyze this whole process, some guy making $3.00 an hour put the original top on, and he was probably hung over when he did it.
No one lives forever, the trick is creating something that will.