theBass:
My first question would be: Are you 'eyeballing' the adjustments ONLY, or are you using rulers, feeler guages, etc.?
From your description, I agree you 'get it' about the dual truss-rods. And I would doubt you need to worry about a neck warp or heat treatment.
Action is made up thousandths of an inch here and there: The depth of the nut slots, the spacing of the frets, the bridge placement, the string heights, etc. AND the amount of bow (or, relief) in the neck.
Until I began to use a machinist's 6-inch ruler and feeler guages (the blade type, like we used to use for auto ignitions), my adjustments were 'eyeballed' and inconsistent.
My adjustment routine follows this method:
Tune to 440 (Remember, tuning is tension).
I check the heights at the nut, or more precisely the string clearance over the first fret. They should measure out like this:
G, .020
D, .025
A, .030
E, .035
B, .035
This is measured with the feelers. If they needed adjusting, I loosened the nut lock screw, raised or lowered the pertaining half of the nut, then locked it back down when I finished.
Re-tune.
Then I measure the string heights over last fret. I go for a 16th of an inch under the G, and 1/8 to 3/16 under the B, by raising or lowering the appropriate side of the bridge. As ALEMBICS use 1-piece bridges, this will induce a slant to mimic the nut heights. Generally you will always need a LITTLE more room on the bass side as the bass strings flop around in bigger arcs.
Re-tune.
Now use a capo to fret the strings at the first fret. I hold the B-string down at the fret over the neck/body joining spot. I now get the feeler guages and find 12th fret. The string is a straight line between my right hand and the capo. I find out what the gap is now. I then adjust the truss rod until I get to a .010 or .012 gap at the twelfth fret.
Re-tune.
Now turn the bass over like a left-hander and repeat this process with the G-string.
Re-tune.
Now, I play with a VERY low action and a light touch. If you prefer a higher action, experiment until you find numbers that suit you. Now you see why I can't eyeball adjustments this fine.
The short version for the less technically-inclined who prefer a higher action is:
TUNE to 440.
FRET each string at the third fret: Raise or lower the nut until you can hear the string just tap the first fret when you press it there while holding the note at the third fret.
RAISE the bridge on each side until there's a 1/8 clearance under the G and B (or E).
ADJUST the truss rod tension until a Fender thin pick will just fit between the string and 12th fret while capoed and held as above.
DONE.
Measuring the relief on each side will allow you to essentially adjust the two truss rods separately, yet identically. This should eliminate any twist. You would SEE the twist in the measurements. On my five-string, the B-side always takes more time, because there is obviously more tension from the E and B, than the G and D.
Two reminders:
After you do this, you may have to 'chase' the neck relief (a few slight turns on the rods) for a few days until the wood takes its final set.
You would need to repeat this if you install a different set of strings than the set that is on at the time you do this. ALL of these are slight turns on the truss rods: A 1/4 turn is a LOT. And try to do the truss rods like your tuning keys: Always tighten UP to where you want it, not loosen DOWN to it; this will 'set' things at tension.
Remember that there is a delicious interplay of tension, heights, and relief. Don't be surprised if this takes quite a while the first time you do this: Over time, you'll become quite good at it, and wonder why you didn't learn this earlier.
Plus, do you really want STRANGERS working on your MK? Horrors!
J o e y
PS Not enough range on the truss rod? Add flat washers under the nut ONE AT A TIME to get a little more leverage.