You could possibly try removing the transfer track and replacing the gap with standard track, then use the "make straight" tool, and then replace the transfer track. You'll likely still have to do some manual tweaking to get it all aligned just right, but will probably be better than manually adjusting the entire length of your brake run. Hope this helps!
Edit:
As I was thinking further, if you wanted to be extra precise about it, you could calculate the coordinates of the midpoint between where the ends of your transfer track will be. Then, set those values as the position coordinate values within the "Special Track Properties" of the transfer track. If you want to take it a step further, you could find the angles with respect to the x, y, and z axes and set those values as the rotation angles within the same "Special Track Properties" menu.
Yes, this is quite a manual process, but all just depends on how straight you want your brake run to be.