One of the things I would change about the controls is letting pick the Yes/No decisions with mouse (if you click on No it will select Yes because it simply accepts whatever was selected). The other is letting player interact using mouse instead of using looking direction of the character (so I'm next to a table and I can't interact with it until I turn to it using WSAD, instead it could just direct player on mouse click and interact as long as it's within range).
The combat is fine as it is. There were other options like letting player play more defensively (as a health vs time tradeoff), so aggressive playstyle actually ends up simple in practice. The timer gives you lots of design options, like getting items from fleeing enemies, destroying crates mid-combat to save time and having different room difficulties with more risky combat but better loot. Running from encounters could be fun too using the acrobatics mode to its fullest and you can always band aid fix it with balanced item drops.