I'll take a moment to dig through this later this afternoon, but I've done A LOT of exhaust simulations on a 500cc single cylinder application in EngMod4t as well have talked with Calvin Elston at length. Additionally, a friend of mine works with Calvin on stuff and another friend has used Calvin with fantastic results. I'll sum up what I have learned the last year in a bit.
Took a bit of a look through this. I can double up my engine combination in EngMod4t. It's for a SR/TT500 engine. I'll use my cam specs, head, etc, just to look for trends in exhaust patterns. This will drag out over a couple weeks as I'm traveling all next weekend.
It seems you're on the right track. Megaphones still seem to be preferred in the single cylinder / flat track world, but seem to be going out of vogue. You are on the right track with the small diameters. Velocity preservation is critical and this goes right back to everything Calvin Elston preaches.
I'm likely going this route, and running it into a smaller Burns muffler than what you have:
With my rpm range (peak at about 7k), I'll be placing it 10-12" from the head/interference.
Calvin did a header for a friend of mine with the Fueling A/R chambers at the first step location. The overall length of the header was within 2" of what it was before. The difference is the tubing off the head went from 1 5/8" to 1 3/8" to match the port exit area. Power was up 10-12% across the entire range and with down a jet size. This was his first time using the chambers in the primaries, but his theory and results with A/R devices like this, is the tubing even smaller due to his belief that you are removing reverse flow, and thus the pipe will have less mass in it.
In EngMod4t, I found stepping the pipe like you did provides a similar benefit as a proper megaphone / reverse cone, but without the bad (and it's lighter and easier to construct). A megaphone really only works with a reverse cone, which really acts as a A/R device. Also they need to be a bit longer than what you have.
To see where things are now with the factories, take a look at the exhausts on the factory Indian flat track bikes.
The factory V&H Harley XG750R (which is a unreliable dog) has a similar looking exhaust into a x-pipe, but without the big step (stepping up kind of like yours does).
I will likely do something really similar, but the double A/R chamber will be (in spirit) where that big step is. EngMod4T has trouble modeling these devices, but I can work it out via just regular steps, which is how the engine should see it. I'll build two pipes though and test back to back.