poor running after stripdown xj650 4ko 1981 (with confessional)

After engine rebuild to sort gearbox, she did |NOT want to fire on all 4, I looked at the pickup coils, and to my shame and horror the baseplate was missing all retaining screws. Replaced them, and she runs on all 4, but not well at all. Could I have trashed my pickups?, rattling around (didn`t ride it, but feeling sick right now). Plugs 1 and 4 sooty, 2 and 3 shiny/wet. It ran normally before I had to pull the motor to fix a gear selector problem. The gap between the pickup and the rotors is .6mm (upper) .9 (lower). I dressed them with a fine file, no difference to running. It will start, but wont rev properly or idle.