I have seen a few of those cast plates crack and peices rattle around in the housing till it busts the pickuo coil. Mattoon makes a billet one. Make sure you use locktite!
The headgasket should be fine and ball joints you cant grease. Flush the fuel (prob already did..) and check wheel bearings and brakes. Once your jetting is good and clutch works right. You should be good...
Yfz shocks ride like poopoo. If all your trying to do is lower it some blaster shocks are much cheaper and ride like poo as well. Rm stators crap out, you can google that one and see multiple testimonials to their junkness.
1 cc wont make a big enough power difference to risk separating that crank and detonating that topend. Get the port work done and true and weld that crank!
Right but if its .060" squish now then that might be your problem. Like if its set up for a .012 base and has a .020 instead. It wont have the torq to get out of the hole like your describing. You dont know till you check...