My example above http://www.vicious1.com/forum/topic/fusion-360/#post-4237 does three passes and two tool changes. It starts with a facing, then does a tool change here to do adaptive clearing:
... N6645 G1 Z15 F2000 N6650 M107 ;Adaptive1 N6655 G1 Z15 F2000 ;T3 N6660 G1 X-20 Y-20 F2000 ;T3 N6665 M117 Change to Tool T3 N6670 M25 ;Pause for Tool T3 N6675 ;T5 N6680 M106 ...
Then a second tool change here to do final parallel finishing:
... N148745 M107 ;Parallel2 N148750 G1 Z15 F2000 ;T5 N148755 G1 X-20 Y-20 F2000 ;T5 N148760 M117 Change to Tool T5 N148765 M25 ;Pause for Tool T5 N148770 ;T2 N148775 M106 ...
Just search though your gcode and you should find some of these commands like the M177 between operations. Are you using an LCD/SD controller?
I will think about the different length tools some more but there is probably a way to offset the Z axis to compensate between tools. Probably an easy way to manually do this by editing the gcode. I will have to put some more though into how it can happen automatically. OK?