By putting washers between the rear cover and the case you introduce play into the system... your conrod can now move backwards on the crankpin, and that means it will also move backwards on the piston pin... this causes a considerable side-load on the piston when the engine is running: THIS IS BAD!

If you haven't run the engine yet like this, then just remove the washers, and pray nothing was hurt.
If you have run the engine, then also pray and remove the washers... and then run the engine to see if anything was hurt. If it doesn't work anymore you probably need a new conrod, piston, sleeve and piston pin.

The one thing keeping the conrod in the right position is the rear cover... it is entirely normal they make contact.