Jess, since the problem[s] occur when it is shifting automatically, as well as manually (with the ES), it sounds like a transmission problem (and not a problem with the electronic shift). Were you doing anything (that you can remember) when this symptom started occuring?
Without a doubt, you should let your engine/transmission warm up before riding your atv. It is designed to operate at an optimum temperature, and not when cold.
When the Fail Safe Relay kick in, it is because something else is not operating correctly. If that is the case, then I'd suggest that you not continue to try to shift and operate it. Otherwise, you could cause further damage - especially if the problem is in the transmission.
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