if its in a book, it must be true!!
sorry, but that is a typical book readers response.
in theory everything youve said is correct, in the real world its not.
resonance tuning works well in a perfectly straight pipe with smooth walls, a constant temperature range of air within it, and setup on a test bench in a laboratory.
we did some experiments at college with resonance in tubes, and even in the classroom the results didnt come out perfect.
in an engine, where there are a zillion dynamic entities, resonance tuning simply doesnt work how its supposed to.
there are formulas to calculate it, but they have variable factors within them that you have to estimate.
there are also complex radii within intake systems which make it hard to even precisely measure the length of the intake, let alone which part of the valve to take as the end! in the real world the formulas can get you reasonably close.
experience and knowing how to read the results of the formula based on the engine in question gets you even closer, and then you use trial and error to find perfection.
most top engine tuners that i know, or know of, dont even use the formula, its that far out compared to what their experience tells them from years of trial and error on a rolling road
(a couple of guys i know were tuning inlet lengths on carbs when i was still wearing nappies!)
as for a plenum setup, again, a book response.
top race cars with the most conditioning of airflow you can possibly imagine, which are built almost solely around aerodynamics, still run plenums.
i am of course talking about F1 cars.
they can make the air go just about anywhere they want with their
£100m aerodynamics budget, PER SEASON.
yet they still run an airbox which has a plenum chamber.
its not your conventional layout, but it still utilises positive pressure to improve cylinder filling.
whats more, there is plenty of space in many engine bays to run equal length long trumpets, but the reason cars come with a plenum as standard is as a cost reduction and simplicity exercise.
running ITB's means no reliable vacuum in the intake.
how can a car idle in a perfectly controlled manner if it has to do so by opening the butterflies? manufacturers are all about emissions and cost reduction.
running ITB's results in poor emissions, not to mention the fuel consumption issues.
an idle control valve in a sealed container on the other hand is much more desirable.
the plenum vs ITB's for ultimate power is a long argued matter which is rarely ever settled with anything more than speculation.
even if someone were to build a plenum setup that out-performed a set of off-the-shelf ITB's
(which is easily done), there is still the argument that the ITB's just werent designed to the same standard as the plenum setup, and vice versa.
it will never be settled properly, but i can assure you that the opinion amongst those in the know is that a plenum is the way to go for outright power, so long as the regulations
(if used in racing) and packaging requirements permit it
finally, on the matter of TVIS.
TVIS doesnt work in that way at all.
tell me where the first resonance peak occurs? the large ports of the largeport head are far too big as standard.
they flow enough air for 180bhp+ without modification, but when youre only running 120bhp this results in low inlet velocities, poor mixture conditioning, and thus a reduction in bottom end torque.
at higher revs the head works much better as inlet velocities are raised.
so Toyota designed TVIS to get around the mismatched cylinder head setup.
it has 2 holes of equal diameter, and below 4500rpm
(the changeover points vary between engine revisions, lets call it 4500rpm for simplicity) one of the holes closes.
this halves the inlet manifold runner area, but since when was runner area part of the helmholtz resonance calculation? length remains the same, all you are doing is forcing the air to move through a tighter passage, and thus improving the inlet velocity at lower revs where the torque needs to be recovered due to the overly large inlet ports.
this isnt tuning for resonance, its just basic fluid dynamics.
in hindsight Toyota realised that the TVIS shouldnt be necessary, and they designed the smallport head which did what the largeport should have done 5 years previous.
they carried TVIS over to the mk2 for a very short while to try and use it to benefit torque on the 3S-GE engine, and whilst it made a small difference
(many claim this as proof that the TVIS was an intentional development, it wasnt, it was an afterthought on the 4A-GE) it wasnt significant enough to justify the added complexity and they dropped the technology
one final extra point i want to add which i forgot earlier
- if equal length runners are the way to go for optimum power, why do Hasselgren run uneuqal length trumpets on their 250bhp 4A-GE Formula Atlantic engines?
and il post a picture i took of it for proof if you dont beleive me, installed in the back of a Swift 014.
my personal belief is that things are a lot more complex than books and simplified scientific formulas suggest!
not wanting to have a pop at you, by all means feel free to offer a counter argument.
but based on my knowledge and understanding, those are flaws in your reasoning
(and the reasoning of those who wrote the books that you read)
of course with a throttle body system drawing air through individual air filters 
ahem.
