Kafin,
as this is your first ARC I would not be pulling the entire engine crutch out. Probably too much work and skill required at your stage of development.
Also, as this is an ARC any height adjustments to the engine will result in a misalignment with the spinner on the nose.
As you are in Indonesia your best fix would bet to cut 3mm off the top of the bearers, place 3mm aluminium plates there and bolt in your engine.
To answer your question, yes putting washers in place to level up the bearers will work. I would use wider washers than you have pictured, but it would work.
Craig