Engine planning 101

Make a plan and stick to it.
Very true how do you come up with that plan? That is what I'm asking for example I'm planning out all the little things to get my compression where I want it. Pistons head gaskets etc. But then you have the valve to piston clearance issue. Everything I read is how to check the clearance after the engine is already completed how can plan for that before you buy the parts? Or assemble the engine? I dont want to spend 1k or more just to find out my valves dont clear my pistons have to start making adjustments.