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E3D conversion

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Looking for info on doing the upgrade / change to E3D Lite 6 Bowden extruder. I print in PLA, have a Jr 1.0w. I use Simplify3D or either XYZ software (the old one or the new suite).

My issue is that "long prints" (read, anything longer than about 10min to print) will start fine but quickly degrade - filament will just not extrude at all after a while. I have a feeling the nozzle clogs really fast because if I unload, deep clean, reload, it will print well again for a few minutes then crap out again.

If someone has an idea of a setting I should (related to temperature, retraction, etc.), I'll be happy to try but I've had the printer for a while and it has printed fine in the past, so unless a firmware has changed something, I believe the problem is due to wear on the extruder.

Otherwise, I thought about buying a new nozzle (they are 70USD on the site) but after seeing what they charge for shipping and so, it amounted to about 160USD... which is about what I paid for the printer when I purchased it new. So I'm thinking of switching to an E3D extruder, which is considerably cheaper (about 30USD + shipping for me).

Other than the physical conversion of the printing head (I've seen the parts on Thingiverse), is there firmware flashing, electronic hacks, etc. involved or it's basically, once it's fitted on the head, it will work?