For the Y axis issue, perhaps try inverting the value of INVERT_Y_DIR in Configuration.h.
I ran into the same issue with the extruder mount too. For a while, I used two large zip ties connected together, running around the back to the front between the heat sink and fan, above the bolts. Then I found that those bolts were able to reach the motor from the back of the X carriage... So I used shorter bolts to assemble the extruder part, without the fan. Then I bolted the fan directly to the heat sink, self-tapping the fins. Then I used the original extruder bolts to mount the whole assembly. I finally got long M3x50 bolts since I wanted to be able to mount a parts cooling fan bracket under the heat sink and have the fan properly mounted.