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Ok! got them both printed. The mount Peg modification on the duct with the outlet split (A?) fits a little better around the wheel nut. But both seem to fit OK, the one on B seems to fit a little closer. I'll attach a photo of the distance from the print bed, looks to be ~3-4mm. I'm not sure if Its just me, but now that I have everything printed it and actually went to screw them together, it looks like the mounting brackets seem to be made for a size M2 bolt , but the holes on the gen3 base seem to want a M3. I've attached the differences between the M2 and M3 bolts that I have. Also, If this is getting annoying, feel free to tell me to bugger off.
Edit: I can't find the gcode that I printed the V3 ender base from. So Its possible I printed something wrong.