What program did you use to create the plan before it was a PDF?
When I make plans in Sketchup, they are actual size. 100%. Then when they are made to PDF the measures are kept one to one. When the poster, or tiled, PDF is printed, it is to scale.
As far as determining the size of your plane, identify your limiting factors (i.e. foam thickness, prop size, preferences) and make the plans based off of that. From reference drawings imported to Sketchup, I get a couple measures that could limit. Prop clearance, cowling size, interior fuselage room, then set that at the size you want it to be sketchup scales the rest. Some people use wing span as the determining factor when it comes to self designs.