Drive blocks were overhauled a while ago. for Tube Screamer types, a dry level was added/implemented as that's how real TS types work - the dry signal is part of the resulting overdrive tone/sound.
so on many drive types, there is now additional dry signal present that may not have been there before. this was in Feb of 2019 and here is the release note:
"For many types there is now a “Dry Gain” control. This parameter controls the amount of “dry” signal mixed with the “wet” (distorted) signal. For a Tube Screamer-based model this will default to 100% due to the topology. For other types this will default to 0. Values up to 200% are allowed. Note that the dry data is added before any tone controls and therefore is not exactly equivalent to a mix but rather replicates the behavior of analog circuits."
not sure if that's what you're experiencing, but wanted to point that out to make sure. i personally have been reducing that new Dry Gain control many times to 0 to get the sound i want.
adjusting the Input Level in the setup menu wouldn't affect any of this, as that adjusts a signal to noise ratio for the input, not actual audible level or amount of signal going into the grid.
i loaded your preset and IR. the clean scene sounds clean to me. no distortion or anything, so i don't think anything is wrong with the preset or settings there. if you have a guitar with active pickups, change the battery as it may be dying and causing distortion from the guitar. if not, can you share an audio or video recording of what the distortion sounds like? with my high output guitar, i don't get any distortion in the clean scene.
when i engage the Drive block in the Clean scene, it's a T808 OD which would have the Dry Level turned up as mentioned in the release notes above. at default setting of 100%, yes there is a strong clean signal going at the same time. it's like a 50/50 wet/dry sound that just doesn't sound right to me. Cliff has confirmed several times that this setting matches the original pedal, so there's that. but i just reduce that parameter to 0% or so and it sounds more like what i'd expect.