Failing slow extrusion after upgrade to E3D hotend
I bet your old and new extruders have different hobbed pulley/bolt effective diameter.
It looks like your new extruder has smaller hobbed diameter that's why it pushes too less material.

In MatterControl application there is a slider which allows user to tuneup extrude ratio on the fly (while printing). You coud check it so it would confirm the issue.

In Slic3r you could go to

Printer Settings > Advanced > Extrusion width

and experiment with it (especially with Default extrusion width)

Both (Slic3r and MC) could answer your question if it's extrusion ratio issue. If you confirm that - you can proceed with calibration. Here is method to calibrate extruder flow and general calibration article here.