Hmmm sounds like two seperate problems, a missfire problem and a knocking problem.
For the knocking its going to be in the tune.
As for the missfire, if you have changed plugs (BCPR6E's?) and it still does it, then most likely it is the coilpacks or the loom.
As for the broken engine earth, there is still a main engine earth on the block underneath the plenum, however i would still add a couple more earths off of the head. I picked up a Pivot engine earth/voltage stabilizer kit for $50 brand new to test it out (retails for $300 on nengun at the moment, f**k that!) and straight away noticed the car was easier to start and the voltage didn't drop down as low on start up anymore. So extra earthing of the engine definetely helps a tiny bit. Add another earth near the coilpacks to the body of the car just in case, it can't hurt.