The thermostat probe does not go in the enclosure. It should be under the enclosure, sandwiched between the enclosure floor and the heat pad. Otherwise your snake can move it off the heat, pee on it, dump his water bowl on it, etc. and cause the heat pad to overheat.
You don't need an inch of substrate. Half of that is fine.
I wouldn't worry about the high humidity, and taking out half the substrate should help. If it remains high you can always add some small ventilation holes to the enclosure.
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