Sometimes it's little things. As I was reading the initial post, to my mind came one of my experiences where I had removed the injection linkage rod that crosses over the camshaft cover to adjust the valves, and although I put it all back, I had forgotten to properly snug down one of the brackets that holds that rod. Even though it was only a little bit of play in the linkages as a result, the engine ran very poorly. That was not your issue, but something a bit similar - small issue with big consequence. Such a relief when you can fix seemingly major things in a relatively simple way.
I had similar problems with my Bronco II recently, where I had neglected to re-attach a very small vacuum line to the intake manifold, and with my son's 300ZX, where two ignition wires seemed properly plugged in, but as I had manipulated the distributor cap with the wires attached to check for TDC, the two wires had just backed out a bit, causing loss of spark and terrible running. It took me a while to track down each of these culprits and I felt silly afterwards. But better this than a blown headgasket or a timing belt that skipped one or more teeth, as had also crossed my mind as possible causes. Then last year, my Pagoda started just cutting out inexplicably during drives - turned out to be a connector of an ignition wire (to the coil) that I had not crimped on tight enough. It seemed fine from the outside, but it wasn't.
