Taking your pedals out will not affect the height. The brake will go where it wants and the clutch will ride based on your adjustment. You want it even or higher than brake. Better to be higher so if your adjustment loosens you still have some travel in your pedal to disengage the clutch.
Engine Test Stand Playlist: https://www.youtube.com/playlist?list=PLwoxyUwptUcdqEb-o2ArqyiUaHW0G_C88 restoring my 1968 Firebird 400 HO convertible (Firedawg) 1965 Pontiac Catalina Safari Wagon 389 TriPower (Catwagon) 1999 JD AWS LX Lawn tractor 17hp (my daily driver) 2006 Sequoia 2017 Murano (wife's car) 202? Electric car 203? 68 Firebird /w electric engine 2007 Bayliner 175 runabout /w 3.0L Mercuiser__________________________________________________________