Can you share some photos of the printer and the over extrusion?
Can you share a gcode file that shows the problem as well?
For good measure can you also share the results of sending M122 and M98 P"config.g"?
So if you only have 2 extruders, then the second tool definition should be
M563 P1 S"Hotend2" D1 H2 (not D2)
This was exactly the problem. I knew it was going to be something simple like that, I just stared at the problem long enough that I couldn't see it. Thanks for your help!