[Seakir]

Interesting project. I was looking at air turbulence and its effects inside an air intake system and came across this a short while ago:

Design improvements of an automotive air intake system

This project was conducted in conjunction with Proton R&D department to study and improve the air intake system (AIS) for the current Proton Iriz vehicle. The AIS comprises of few parts: snorkel, a...

aip.scitation.org

It says they made 3 designs to the air box of the model in question used for the analysis, to see which gave better performance and 4% was the best they achieved for design 1, but doesn't show the design- grrr!

However, they state air delivery is weakest at the point where the air turns from laminar to turbulent, which is inside the air box/filter housing itself. With this in mind, are you plugging your new pipe into the standard entry hole for the box, or are you redesigning the box itself?
If using the plastic standard entry, I would say the cut wouldn't matter as long as you can get enough grip with the jubilee clip/band on the pipe that will be used to seal them airtight.
If a redesign, then maybe the angle cut might be good to consider, as long as the travelling air isn't given a lip to get trapped by to create turbulence.

 

[Seakir]

I got no idea on how the uneven lengths of tube affects resonance, except what logic might guide- if the pipe is smooth the acoustics and pressure should be equal, but at bends the dynamics are going to change and yhe sound -depending on the material containing it- will react in different pitch where air is compressed at these bends. Your bends look clean though, so I would guess that with a little experimentation, you will find that resonance you're after.

The reason for asking about an air box mod is that I've tried a k and n filter in
my wj variant using the standard box and tbh, I noticed no acoustic difference, even when the turbo kicks in. I think that a closed air box might muffle a lot of the air being sucked in and the acoustic sound/grunt from a k and n/sports style air filter, which is why I took mine out and put a mopar filter back in as there seems to be no difference with mine regarding performance either.
Now, when I did a cold air intake mod with a cone filter on a Gasoline Ford cougar v6 a few years ago, that really opened up the acoustics and you could hear the air being sucked in ten times louder.
Not sure what others would recommend, but maybe a cone with no air box might be worth looking into? (Thinking about it, I've still got that cone filter from the cougar set up. I might have an experiment with it and take out the air box, to see what an open set up in my diesel lump sounds like. Kudos for the idea 👍.)

 

[Seakir]

Oh I see. Keep the standard box for sure. Now I see that you're looking for performance and air pressure ratio being as equal as possible down the pipes, therefore making it as less restricted as possible?
I would go with your instincts regarding your mod therefore, as it seems you've done the math and know your stuff- maybe experiment with both cuts you're considering? One thing you could try, in order to do this, is to buy a 3 inch exhaust sleeve and another air box from ebay. That way, you have the means to correct pipe work by using the sleeve to connect end sections of your pipe should you find your end cuts wrong- the extra layer of metal, considering its an exhaust system part, might also help keep the air cooled somewhat by adding another layer of insulation, but it might be worth remembering it could also trap heat if idling. Heat wrap for exhausts could also be another option, but I would go for heat resistant paint and coat it over the air pipe. Go for a nice colour 👍(I painted my cougar exhaust and manifolds in a nice flame red.)
Also, it won't matter too much if you're hacking into a box brought off ebay and you'll also have spares to fall back on should you need them or want to keep your mod if you come to sell the vehicle.

The horn cap sounds a good idea to create less turbulence- the easiest way to visualise air movements is to imagine it as water flowing -they follow the same rules of motion, just different textures but same force/pressure relationship.
In this context, maybe treat the pipe connection into the air box like a sinkhole, so air is funneled in like when a plug is pulled in a sink?