All WagonRs suffer from the same problem and I don't think there's a way around it.
Triple cylinder engines require a counterbalancer, otherwise they shake and rattle. That's just physics, my friend. From a mechanical standpoint, a triple cylinder engine is a very VERY bad design as its inherently unstable. I'll explain why:
In a 3 cylinder engine, piston one (the front piston) reaches TDC (Top Dead Center) while the other two pistons are 120 degrees away from either TDC or BDC (Bottom Dead Center). Take a look:
In this picture, the left piston is at its TDC, while the others are at their BDC. What this all means is that the primary and secondary forces are balanced vertically, but the torque over the reciprocating pistons is unmatched, very much unlike a typical straight-four engine. Instead, the engine is trying to naturally rotate and flip over on itself (Like a monkey, if you will), hence the vibrations you're noticing.
So, don't worry about the vibrations. It's all part of the WagonR packge, so to speak!
