Thank you for the various pointers, they definitely helped. Even trying out different slicer (Prusa) and seeing the same behavior helped rule out some causes.
Cause of Under extrusion was my e-steps being factory reset to 93. No idea when/how that happened. Haven’t updated firmware, and don’t recall reseting settings for any reason. I don’t see M92 commands written to any of the gcode files I’ve printed (yeah, I cache them…). 
Fix was to set esteps back to ~141, something I did June '22 back installing Dual Gear Extruder before kicking off my LR3 prints. E-Steps change is needed since the gearing is smaller, bonus is higher torque. Followed info from Teaching Tech (and others).
Symptoms I should have paid attention to earlier :
- Prime line at start of print was much thinner than usual, with some blobbing.
- Skirt was pathetically skinny.
- Wall separation (delaminating, not sticking, bonding, etc…).
Ideally, earlier on, should’ve :
- Check configured esteps, use M503 in terminal. For me, my Marlin output should contain E141, e.g…
Recv: echo:Steps per unit:
Recv: echo: M92 X80.00 Y80.00 Z400.00 E141.00
- Check 100mm extrusion was flowing as expected, was actually 65mm instead of expected 100mm. Discovering this earlier would’ve avoided unrequired nozzle/ptfe related changes, a distraction which I’ve rationalized as overdue maintenance.
Had no reason to suspect esteps had unexpectedly reset, so I ended up doing many pointless things before discovering Ender firmware setting. Tried various things to troubleshoot and figure out cause(s):
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Changed many temp, flow, layer height, nozzle width, fan and other settings. Cloned profiles with date in the name to use as reference, and undo/revert regressions.
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Multiple cold pulls.
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Completely cleaned out heatsink and hot-end using scrap PTFE. Wiggle 'n push PTFE through several time while 240C, wiping off plastic remnants. Required removing nozzle, PTFE and PTFE end fitting. Did this process twice…
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Changed pneumatic fittings for the PTFE ends. Stock ones were being trashed by tubers.
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Changed to new 0.6 nozzle.
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Changed to new Capricorn PTFE. Friction of the original seemed ok, but changed anyway…
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Tried two different PETGs, even tried PLA once I realized extrusion distance was the problem.
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Carefully lubricated moving parts of gear extruder.
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Ensured gear extruder mesh in contact with filament was thoroughly dry/clean, no debris/flakes/oil/dust/etc…
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Verified Extruder Gear Grub screw wasn’t loose. Used fine permanent marker to draw line on Stepper shaft and gear. So easy to visibly spot slippage.
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Adjusted gear extruder spring tension, several times. Enough to grip, but not overly crush, using subjective naive judgement of course.
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Finally mentally clicked to check esteps when I noticed extruding 100mm was consistently wrong by ~35mm. A huge amount that made me suspect some serious blockage was happening, except the distance was consistently wrong… So, I finally checked esteps, calculated correct value, double checked Dual Gear Extruder product page which suggests e-steps be 139, then had the aha @$%* moment of cause and fix.
At one point, to eliminate possible causes, had completely removed PTFE, pneumatic fittings and hotend from possibly dragging/blocking extrusion…
Finally have strong walls again that refuse to separate, even when shanked…
While troubleshooting, to rule out arachne, I modded the original Voron clip to have 1.8mm wall instead of 1.6mm for my 0.6 nozzle back when wondering whether arachne was a factor. fwiw - Shared slightly stronger clip on Printables.
Hope this helps/entertains, cheers!