Hmmm.... I think if I run thru this from first principles, it might help
to clear up any misunderstanding...
Throttle Bypass ScrewsThese operate quite independently of any other adjustment to the ITB
and when opened, allow a tiny amount of air to bypass the throttle plate.
They are a "trim" to compensate for any small differences between the
amount of air leakage around the fully closed throttle plate on each ITB.
They are not intended to be used to compensate for differences due
to the incorrect adjustment of the throttle stop screw or linkages.
Throttle Stop ScrewsEach ITB is provided with a adjustable stop screw on which the throttle
arm comes to rest. Essentially, the throttle plate should come into contact
with the throttle bore at exactly the same time as the throttle arm hits
the stop (zero clearance). This makes sure that the throttle plate is
completely closed, but prevents it from impacting on the throttle bore
and cutting a groove. The throttle stop clearance has to be checked, and
reset if necessary,
before any other adjustments are carried out.
Linkage Opening ClearanceTo ensure that all four throttle plate open at near enough the same time,
the opening side clearance is set to 0.03mm. Thus the #1 and #4 throttles
open a tiny fraction later than the #2 and #3 throttles. The Return side
clearance in not critical and is set much larger, as each throttle has its
own return spring, and does not rely on the linkage to "push" it closed.
So, on to your questions...
1. It is possible that if the throttle stop settings of linkage adjustments
were out, someone may have messed with the bypass screws to try and fix
the problem. If you got a wide variation in flow with all the bypass screws
all the way in, then I would say that is what happened.
1a. "Fully closed" is set by the throttle stop screws on each ITB. After that,
not being fully closed is caused by the incorrect setting of the linkage
opening clearances. If you could remove the linkages to eliminate them as
a variable, then set the throttle stops (bypass screws all the way in) you
should have near enough to zero flow. But because nothing is perfect, there
will be some small degree of leakage around the closed throttle plates, and
once you have used the bypass screws to balance for equal leakage thru each
throttle, you might measure some very low flow rate on each.
2. Yes.
3. Refer explanation above.
4. I will leave it to you to decide

It is an awkward job just seeing what
you are trying to adjust, and with less that four hands to hold a light, feeler
gauge, hex key, tiny spanner and rotate the linkage to a point where you can
get at the adjusting screws.... I found it easier to do on the bench.
4a. I'd say that it is probably rich at idle because the extra air leaking thru
the throttles is dropping the manifold vacuum and the ECU is adding extra
fuel. I found that once I got my throttles adjusted correctly, my ISCV had to
open quite a few more clicks. The fact that your AFR's are normal while
driving says that your ECU is most likely working OK. BTW, you shouldn't
be working in the garage with the engine running and the door closed !!!
Cheers... jondee86