Quick update, finally got the FJ40 running and idling smooth. Timing is all set and I finished half of the final running valve adjustment. All I have left to do is finish the the passenger side valves.
So far all of the previous issues are gone. No detonation/valve chatter, no single tick when I turn off the motor, all the pistons are firing perfectly. Can't wait to test drive it tomorrow night.
On another note....I really like the MSD Digital E-Curve distributor. After I learned how to set it up it's so easy to deal with. Nothing like being able to change the curve in just a few seconds.