Turns out my flywheel had come loose. All the 8 bolts were loose enough to give the wheel about a 1/4" of play and make a horrible clunking noise

This might be bad news. If the flywheel moves around on the crank enough, one or both become junk. The flywheel needs to be a .000" fit on the crank else it will always come loose.

Between shifts I got a little plume of smoke.

Valve guides and/or seals, don't worry about it.

My rings are fresh. The cylinder walls had some minor scores.

What rings did you use? How was it honed?

1 and 4 are burning pretty hot/lean (a friend told me this) as they had a grayish look compared to 2 and 3.

The inner & outer cylinders do run slightly different, that's typical of any inline four with twin SU's due to the firing order.

Whats with the lack of decent rockers?

They are all 35 or more years old! You can re-radius them once when you do a valve grind.

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Three 164's, Two 144's, One 142 & a partridge in a pear tree.