I have exactly the same model fitted with a Thunder Tiger 46 PRO but I had none of the problems with the assembly which you had and mine has the tricycle undercarriage. I don't consider removing 2mm of plywood that difficult and you can use a small file in a confined space with short strokes. Having said that I built my first model aeroplane at the age of eleven and I'm seventy-four now so I've benefited from a fair bit of experience but at least you've managed to assemble the model ready for flight despite some difficulties.
I wouldn't bother trying to convert a simple 46 two stroke engine.if I were you. What you save on the cost of fuel you lose on the cost of conversion and engines below about 20cc ( a120) don't seem to convert well.
You don't say what flying experience you have but if you've never flown a balsa and ply model please let a more experienced pilot fly the maiden flight for you. Better still, join a club if you're not already in one, that way an instructor can take you up on linked transmitters, the so called buddy box and he will be able to take over control when you make a mistake. Flying a model aircraft is not as easy as it looks and even if you can already fly an electric powered foamy, the Boomerang has a much heavier wing loading and flies quite a bit faster. That said, its semi-symmetrical wing section allows it to fly in quite a breeze.
Picture below of Your Humble Servant on the right with the Seagull Boomerang after its maiden flight.
