Air cleaner is clean, first thing I checked. BUT...... I was staring at the engine this morning and noticed the fuel filter had very little fuel in it (clear plastic casing). So on a whim I replaced it, then cranked her up (new filter filled up quickly). I let it sit and idle until at running temp and gave it a few revs and it ran fine. It also re-started at the bump of the key (it would not re-start after bogging down to shut off before). So all along I could have just been starving it for fuel.
UUUUGGGGHHHH - If this was it all along, I kinda feel embarrassed. Then again, I'm not a mechanic, just have loved FJ40s since I first saw them as a kid, and on an impulse bought one sitting on the side of the road for sale, but did not run. With the help of a toyota rep down the street, forums such as this, and research, I replaced a lot of parts, including the head, it has been running great (3+ years) and loads of fun. Even though I think the engine is tired and does not put out the power it should, it is smooth on excelleration.
Tonight I'm going to re-check timing at engine temp and then take it for a drive. Keeping my fingers crossed.
Thanks.