Since my last posting, there have been further troubleshooting with the prototyping machine. Ultimately temperatures were spiking in one of the jets and causing the heaters to fail while it was printing a layer. This meant on small parts it worked ok, but on large parts the jets would stop firing halfway through a layer as the material in the lines would cool and harden. So, another replacement part arrived yesterday - a control cable for the carriage that holds the jet.
After replacing the cable, it looks like the prototyping machine is finally fixed - and it could be that this bad cable was the source of many problems with the machine over the past year. Of course rooting out the problem has had me replace just about every other major component in the machine, so maybe with all these new parts, running jobs will go a lot smoother.
A lesson to learn when working on electronic hardware. Before closing the case all up, turn on the machine and make sure everything you've installed was installed properly. I'd have gotten an extra hour of sleep had I done that simple test...
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