I don't know what the Toyota 3.0 engines are like regarding interference for the valve covers, but I'd suggest going back over your vacuum hoses to make sure they are in the right places. I've had VERY weird things happen with misplaced vacuum lines. I wish I knew to check those before pulling the top end apart because of the symptoms on my old rig...

Did you replace the PCV valve and reconnect the hose when you were "in there?"

Those are relatively easy/free things to check and are where I'd start.

73
-Jon
KJ6GVM

As seen on Expedition with TX plates: VEGETARIAN - An old Indian word for poor hunter

Grampa's Trooper
1974 FJ40
1987 FJ60