Re clearances. We receive a clearance at the start of the day under an agreement from Swanwick where we are given a squark & frequency. Don't know if this counts as a clearance per say.
On some flights I am flying in IMC for some portion of the flight so I guess I can log this, but it seems the feeling on logging say 40% of each flight is a bit rich!
Log instrument time for that time when you operate the aircraft by reference to instruments. Don't log it any other time. Whether you're on an IFR clearance or not...who cares? Instrument time and experience is about proficiency. The amount of time you spend operating by reference to instruments speaks somewhat to your actual instrument experience...whereas the time you spent on a clearance does not.
If you flew by instruments, log it as such. If you didn't, don't.