Sounds like something that should be able to be fixed! 
A couple of questions (which might lead you to an answer)...
* To clarify, by 'calibrated your z-axis', do you mean you've levelled your bed and got your first layer height looking good?
* When installing the e3d, did you update the firmware to use the correct thermistor and allow for an increased maximum temperature? If you haven't changed the firmware, the temperature set/shown might not be accurate.
* Have you done a PID calibration to make sure the extruder temperature is nice and stable?
* What temperature are you using to print? ABS I assume? Normally the temp is set a touch higher on the E3D than on the stock solidoodle extruder due to the way the thermistor is mounted (230-240C on the E3D is pretty typical).
* Have you calibrated your extruder steps-per-mm (ensuring that when you ask for 100mm of extrusion, 100mm of filament goes into the extruder)? This is important, and could have changed a bit with the new extruder!
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi