Case,
I'm pretty much in agreement with timing chain theory.
However, humor me,
Before you pull the front cover, make sure you pull the valve cover and check for a broken valve spring on that cylinder. Just a hunch. If you have an air hose with a compressor, go to the parts store and get a plug adaptor. This screws into the cylinder where the plug would be. Plug on your air compressor hose. The air pressure keeps the valves from dropping into the cylinder. They make a special tool that by removing a rocker arm, putting the nut back on you can remove the valve spring keepers and the valve springs to inspect. A ball joint fork will work just as easilly. Physically look at both those valve springs on #1. One may be broken and you don't always see it at first especially with the spring not under pressure. At a minimum, look at the springs while you're cranking the engine over a few times (remember, pull the coil wire unless you enjoy a face full of oil).
Timing does some strange things, but so does screwed up valvetrain. I keep going back to you talking about how smooth it is until you plug in #1. There is something to that IMHO.
Also, I'm shell-shocked. A few years ago I had a valve spring keeper sheer on me (not even going fast, just cruising down the highway) and by the time I heard the noise and reached down to turn off the key, the valve dropped into the cylinder, the piston hit the valve a few dozen times breaking the piston up into about 10 pieces leaving the rod and wrist pin to quickly beat a hole in the side of my cylinder wall, ruining a really good Mexican block. All the high nickel content and strength of a Mexican block didn't stop a rod from doing it's harm.
So, yeah, call me paranoid on valve type issues.