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hercek
The best approach is to use right threaded screw on one side of a rod and left threaded screw on the other. Glue the screws to the rod. Then screw the ball joints at the screws. This allows you to adjust the rod length precisely. Otherwise (if you would use the same threads on both sides of a rod) you can set the rod length with the precision of pitch/2 only (that means 0.25 mm for M3, not very good).
Marlin firmware can be easily updated to support different rod length for each tower (Repetier even supports this out of the box). But rods connecting to the same tower must be the same.
I use the m4 set screws as a method to recover the traxxas arms if I ever need to replace the carbon rods. It also helps to align the traxxas with the tube. When replacing arms, I use a razor and cut a slit on both sides on the end of the rod, and the traxxas end with it's fully epoxy covered set screw just slides out. Since the set screw has cured epoxy on it which is of the correct inner diameter of the rod, I can re-epoxy it and just slide it into a new rod. When I remade my rods a few weeks ago, I fixed one end by letting the epoxy cure on one side. Then the other side I adjusted the length via pulling the traxxas rod with inset out until the correct length was reached.
DinoK
Heat can always work to remove glue, most epoxies will start to get weak at around 500 degrees, unless they are high temp. Your experience is very similar to my first attempt. I had a jig that only fit one rod at a time, and it had a flaw that would allow different lengths. When curing I could not see that some of the rods had shifted during curing and had become shorter or longer. The next time around, the carbon was cut together in my bandsaw, and they were epoxied and cured together. One thing that I would recommend is filling the rod to make it rigid. I bought some dessert sticks that were the correct diameter for my tubes, coated them with epoxy and slid them into the tubes when I was remaking them a few weeks ago. The rods are now a sandwich panel and will benefit from the I-beam effect. I recommend this step to anyone.