What is the difference between Full Throttle Height and Critical Altitude?

Bob Tait explains it perfectly:

Every turbo charged engine has a rated boost which is the maximum manifold pressure permitted for that engine. It is marked as a red line on the manifold pressure gauge. Because the ambient density drops with altitude, there will always be an altitude beyond which it will be impossible to obtain the rated boost. That is called critical altitude.

However the aircraft is still capable of climbing beyond that altitude but the manifold pressure available at full throttle will be less than rated boost. For every value of manifold pressure there will be some other altitude beyond which that particular manifold pressure will no longer be available. So every value of manifold pressure has its own full throttle height. Critical altitude is simply full throttle height for rated boost i.e. the red line on the manifold pressure gauge.