1405 lean at WOT

I agree the WOT is lean, but since its in 1st gear it's not likely at maximum loading. It's somewhat common for WBO2 to indicate a higher AFR at WOT in the lower gears than in top gears. It depends on the combination. But regardless, 14:1 is too lean.

Get the WOT full load mixture where it will make best power. This requires a dyno or 1/4 mile run. That's the jets.
Lean the cruising at 65-70 mph afr as much as it will tolerate. Make it a hair richer if your not sure. That's the jet and rod size combo.
Then if you want you can experiment with the step up springs. Factory Chrysler engines were relatively efficient. It shouldn't need to enrich until something around 8.5"Hg or even a little lower. If the engine has been hot rodded or intake manifold change, then it might need enrichment as early at 10.5"Hg. See the post linked above about 'power valve tuning' and the second log in this post showing crowding vacuum.

The vacuum readings here are 1-2" lower than what my analog gauge shows.
I've found the same. I don't know its in the nature of the vacuum system or how the MAP works. With Logworks the table can be adjusted. In general I just live with it. Since you drive in a location with very different air density (eg high altititude) the table can be, and probably should be adjusted to start the vacuum reading from the actual local atmospheric pressure. Depending on the particular logger setup, its may be possible to have the MAP sense the local absolute pressure and then with the engine running provide vacuum reading derived from the actual difference. Is this an LM1 with a LMA-3 Auxbox?

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There will be a pump shot down spike at any accelleration beginning from a low throttle position.
The pump shot is fine for now. You can come back to that later if you want to attempt finer tuning.

When the throttles are closed or slightly open, the fuel is supplied by the 'idle circuit'. The 'idle circuit' delivers most of the fuel when cruising at less than Interstate speed. It doesn't take much power to keep a keep moving steady on flat roads.