Hey Chris! How are you?
This is a pretty interesting topic, i think. I can share some thoughts on the subject which may help you.
Quick note: i`m a student of Mechanical Engineering and most of my background comes from there, as well as a lot of research into IC engine design and machining.
You have two basic problems in engine design, and not in just model ones but any IC engine: Geometry and Manufacture
Geometry will concern all the mechanical elements of the engine (as distinct from thermodynamic or cost elements, etc). The problem here is getting the parts to work together as intended (motion analysis, interference, fits..etc) and to able to assemble them. Some machines can be sound in theory but are not `buildable`. But then, build-ability spills into the next category, which is manufacture:
Manufacture will deal with available materials, machining capabilities and cost (time and money). You can have a great design, but it may take advanced machining techniques, or exotic materials, or be really time intensive.
Taking these two considerations into account you should be able to design a working engine. It does not take much to make it work and there is a wide range of `what works`
then, after your design works mechanically, you can start to deal with optimization...reduce fuel consumption, add power, etc.. but most model engines are only meant to run reasonably well, and that may be beyond the scope of simple designs.
if you do have a full scale engine and try to make a model of it most of the problems you will run into are scaling parts for manufacture, things can get waaaay too tiny way too fast. so you may have to enlarge parts...simplify subsystems (for example, three piston rings can become one, or none).
also, have in mind that power scales to the cube...so a 1/3 scale engine will put out 1/27 the power of the full size one (assuming same working pressures) , while working pressure will stay the same, tensile strength will scale to the square and beams are weird but should scale more to the square than to the cube. that means that you`ll probably end up with a over-built engine when scaling down. and that if you wish you can re-calculate the strength of the parts (which is labor intensive unless you have a CAD program).
there`s much more room to complicate things here, but you don`t have to. you can just scale down, simplify the stuff that gets too small (thinking diesel fuel pumps and injectors), run it untill something breaks, modify that part, run again..(experimental iterative design...it IS a valid tool)
most model engines also run without any load...that adds to the `overbuilt` factor too.
that`s a brief intro i guess... feel free to ask me to elaborate anything.