At this point I do think it's something machine specific rather than a firmware issue, I definitely had some settings wrong to start with and after a lot of tweaking recent prints have been at a good quality. It's the first printer I've built so I suspect there will be mechanical issues where I've not got everything lined up perfectly. In the future I might replace the printed corner brackets with metal ones to increase the rigidity of the printer as it does shake a bit more than I'd like at the moment.
I'm using a 0.4mm nozzle at the moment but also have a 0.6mm. In my previous tests the larger nozzle showed much more exaggerated over-extrusion at the start of each line/layer. I think this was primarily caused by a slicer setting I had enabled "Adjust printing speed for layers below x sec" which paused at the start of each layer when printing small objects.
I've decided to leave to the extruder value at 837 for now and just tweak the multiplier in Simplify3D, I get good infill and top layers with 98% extrusion with this particular filament so it's very close.
The only settings I change for my other printer in Simplify3D are retraction speed, retraction distance and temperature (around 20 degrees higher due to the hotend and dodgy electronics that don't maintain temperature accurately) . I think this eliminates the as a slicer issue but I will do another test print on my other printer to make sure.
I have printed a temperature tower recently with this filament (FilaPrint Premium PLA) and I've got it set at 202 degrees. Oozing is definitely more of an issue with the E3D hotend compared to the Micro Swiss All Metal Hotend I have on my other printer, which is why I've tried to keep the temperature down.
My printing speed is normally 40-50mm/s depending on what I'm printing, I'm usually after a reasonably good finish rather than speed.