Hello,
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For the 4649T: I just use the Jeti integration cable and do not need to plug anything into the smaller connector on 4649T?
Yes, you are right.
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For the HW25A: I use the Telem UNI cable and wire to the shorter, three-wire connector on the HW, I do not need and will not use the longer 4 wire cable on the HW, the one with two connectors on it?
No, the cable with 4 wires is the throttle signal + RPM output cable (single wire). In order to control the ESC, you have to connect the 3-wire plug always - this is the most important thing.
In your setup it must go to the AUX port as there is Throttle output from the unit.
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What do I do with the yellow cable since the 4649T is already connected to A on the uSpirit?
You can connect the yellow wire at the PIT pin, then you can use Governor from the unit. Or you can leave it disconnected when using Governor from the ESC.