You really don't want more than 1/2" of substrate over UTH. It becomes "insulation", preventing the UTH heat from rising into the enclosure where it's needed. And it can also cause the UTH to overheat & malfunction- especially if you also failed to ventilate a little under the enclosure/tank, as the manufacturers generally instruct.
You need to assume that your snake (any snake) may dig down & contact the actual floor, so you want to make sure it's not too hot- that's how snakes get burned. They don't realize damage & remain in place too long. I'm having trouble telling if what you're describing in the new "split-level" is safe or not for him. You supposed to have the t-stat probe outside the enclosure, sandwiched between the glass/or whatever the floor is made of, & the actual UTH. It doesn't matter much what the t-stat is reading, what's important (essential) is that where the snake WILL contact the floor inside the enclosure is not over 90* (or by very little), because sooner or later, they WILL dig around & contact that- & if it's too hot, they get injured. So you need to actually push the substrate away to take the floor temperature, then put it back (not too deep) after you're sure that the temp. is safe.
So off-hand, I'd suggest moving him back to his old home for now
IF you need to make some more adjustments. Like I said, I'm not totally sure what you meant. If he's going into shed (& he's obviously not digesting either) he's mostly going to be laying low right now anyway. If he seems comfortable, this may work out just fine to leave him be.
There's no hard & fast rule about slowly transitioning a snake to a new enclosure (& most people never think of doing it), but it makes sense to do so if at all possible, knowing that snakes keep searching for their old home for a while, & usually refuse to eat as a result. Confusion is stressful for them, & they don't understand where the world they knew just disappeared to. But if your guy is drinking water & seems comfortable in the split-level, I'd leave him there, as long as you don't need to adjust things for healthy & safety, etc. (as discussed above) So again, it's up to you.
Raising the humidity some, & adding some of his familiar furnishings sounds good-
