Maybe this can help
I am not sur this will help, but I have a Makerbot with the Mk IV extruder and 3mm filament.
I have had good result with ABS, but not so great with HDPE.
This is how I calibrated mine with replicator v21.
First thing, check that all your axis are well oiled.
Next, select the following modules (and disable the others).
Carve, Bottom, Clip, Comb, Fill, Inset, Raft (though I don’t use it much more), Speed, Temperature
Now, concentrate on these four parameters :
Layer thickness, flow rate, feed rate, width over thickness.
The first two parameters mostly depend on the machine, that is you won’t have to change them a lot afterwards.
The last two are your main action points.
I started my calibration with these settings (ABS).
Carve\Layers From = 0
Carve\Layers To = 100000
Carve\Layer Thickness = 0.4
Carve\Perimeter Width over Thickness = 1.5
Fill\Diaphram Thickness = 0
Fill\Infill Width over Thickness = 1.5
Fill\Infill Solidity = 1.0 (read further down)
Fill\Infill Perimeter Overlap = less than 0.25
Temperature\All Settings = for ABS, it is normally 220° but Mk IV extruder is not precise. I use 180°. Mk VI is supposedly much better.
Speed\Flow Rate = 255 (maximum)
Speed\Travel Feed Rate = 50
Speed\Feed Rate = 40 mm/s
Now select a full 20 mm cube. Don’t use the wall only version.
The idea of the calibration is to work under the worst case. Extruder speed (flow rate) is maximum (255) and you will modify the feed rate and the width over thickness to get a “perfect cube”, that is, not too much or too little plastic. Most important is the infill solidity at 100%.
Make a test run.
If you have too much plastic, increase the feed rate. If you have too little decrease it.
Adjust the layer thickness only if needed. Modify only one parameter at one time.
Work as much as you can with the feed rate at first.
Let me know if that helped.