So I should have looked closer at the gcode before but it's actually quite messy so there could be this
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Anyway I setup a wipe tower for both extruders. Created a 40mm wide, .4mm thick pipe, sliced it in the place i want the wiping to happen with the two extruders separately, extracted the gcode for 1 layer for each, deleting the G1 Zx.xx instructions, and created a macro called wipetower.g executed on every tool changes. In the macro depending on the tool selected it will extrude the corresponding circles (2 lines wide for .2mm nozzle and 1 for .4mm) at the designated place.
Will test and report
I also redesigned the cooling system that i was not really happy with, should be much better
I'll definitely look into having smoother walls for the organic support but I don't think we have much control over this...