Theres definitely a gap between software and the real world. It's riddled with bad data. This is where the software looks bad. Modern engines which are built and tested in software do exactly as the programs say.
In this situation, we are fortunate. We've got 3D scans of the DTR125 cylinder, head, reeds, and other parts avaliable to all of us. Thingiverse.com houses these models. The information below should be doable while providing realistic power.
For a well tuned mind that doesn't want to spend money expensive programs, The porting-calculator from www.porting-programs.com is a great starting point.
It takes time to get models up and going in simulations, So that'll come later. For now, lets focus on target realistic numbers.
An RPM of 10,500 is about the highest reliable(with modifications) limit of the motor. Ring flutter starts to become a light concern. We'll set peak power limits at 10,500 RPM. Over rev may shoot into 11k range, but thats OK in short burst. Power will drop after 10,500 RPM. 12k RPM is mechanical redline with quality 1mm thick rings.
The first thing we'll need to determine is the Cylinder head design. Theres many different chambers out there. Hemispherical is a great all around design. This is your best everyday design. Conical makes strong power closer to it's target MSV, then it drops off drastically. This is a stronger but narrower RPM design.
Torridial is another that makes very good power, but it runs hot. A more of an all around design.
A hemispherical head is the target here. A BMEP of 10.5 and a compression ratio of 10.5 @ 1000ft of elevation should yielf right about 150PSI. This is plenty of high RPM power.
MSV (Maximum squish velocity) is the speed that air/fuel leave the squish band. If this is too fast, detonation sets in. Higher octane fuel help this a little bit. The higher octane shines in overall compression. Our target MSV will be 21M/s @11500 RPM. This is to compensate for over rev.
With a 56mm bore, 50.7mm stroke, Exhaust port @ 196 degrees. A squish that I would run would be .75mm on the outer and 0.86mm on the inner with a 6.5mm wide squish band. This is subject to change depending on head gasket thickness. Raising and lowering the jug using base gaskets will help correct this. Turning the the jug on the lathe is another method.
This should yield about 155PSI depending on elevation and atmospheric conditions.
I'll focus on the porting program. This creates the target numbers we'd want to see.
With a 155 PSI Target and 10,500 RPM limit, we need to select port shapes and area.
194-196 degrees of exhaust are the target numbers. The lower and wider the better. We'll use 194 degrees for this. You can measure this is a degree wheel or a depth guage. 25.32mm from TDC to the top of the port.
The total exhaust area needs to equal 920mm^2. This is everything including the auxiliary ports. The more square the port roofs are, the better.
The blow down area, the exhaust are above the transfers, Needs to consume the majority of that at around 640mm^2. The size of the auxiliary ports will be computed after the transfers.
Transfer size. I'd go with a combination of 130 degrees on the ports and 132 degrees on the boost port. A total area of 1074mm^2 is desireable. This is difficult to pull off depending on exhaust port width and piston ring end placement. These sould be 38.61mm from TDC.
The boost port, the ony closest to the reeds, needs to be angled to point at the spark plug. 131 degrees here would be a choice. It's area comes out of the transfer area. Both are considered intake.
The transfers roofs should sit 12.1mm above the piston at BDC. The Auxilary exh port roofs should sit 25.38mm above the piston at BDC. There needs to be a gap between the transfer roof and the auxilary port floor to prevent short circuiting. 5mm of space is plenty. 12.1+5=17.1mm above BDC for the auxilary port floors.
Exhaust Port Chamfering. Don't do it. Only a relief needs to be added to the port edges. This can be done with a handfile. The edge of the port should sharp, but moved inwards a fraction of a mm. The relief needs to go upwards from the port a couple of mm. A chamfer only benefits the rings at the very edge where the rings barely protrude into the port. A relief address this very edge. The reason for keeping a sharp edge is for the sonic power of the return wave on the pipe. The hard edge promotes a louder sonic boom, a soft edge causes this to disperse.
Crank case comrpession ratio needs to be adjusted. 1.1:1 to 1.2:1 is a good target. To high of a pressure will cause pumping losses. Check the volume by filling the bottom end with oil while the rod is in BDC.
The angle of the transfers is critical to high RPM. A roof that is angled about 30 degrees upwards and is targeted to be 30% of the bores width (16.8mm) infront of the boost port is ideal. You don't want swirling or anything like that at high RPM. That doesn't promote flow, it hinders it.
Next are your reed petals. High volume reeds that have harmonic resonances within your target RPM range are great. They're a pain to locate and create. Any modern 125 MX bike will have reeds that can handle the RPM. Vforce reeds are a great option and are prefered. The small petals have a high resonant frequency and may be the best at sealing with high RPM. Most reed petals don't actually seal at 10k+. They only flutter.
Carburation. This needs to be the smallest point in the entire intake. Carburators opperate off vacuum. Any restriction before inhibits flow, any restriction after inhibits flow. Your intake tract from the carburator to the cylinder should increase in cross sectional area. Tip area of the reeds should be greater. For a build like this, I'd look into a 32mm carb for more mid range power and a 35mm for pure top end power. Boring bottom end power will be a thing of the past with a build like this.
Flywheel size. This is a topic that doesn't get discussed much. Most people leave it alone. Theres not much math avalaible. A smaller flywheel with a less mass favors higher RPM. A heavier flywheel favors lower RPM. Both flywheels can spin at 10k, and both can spin at 2k. Flywheels are simple a mechanical battery. They store energy in the form of motion only to release it later. They are fairly efficient at it too. But, like newton said, it takes energy to make something move, and it takes more energy to make something bigger move.... Ok, maybe those aren't his exact words, but it's close enough (object at rest remains at rest unlkess... You made it this far, you get it.). Back to the battery talk. Your motor produces most of it's power from about 15 degrees of rotation. The remaining 345 degrees of rotation it is free spinning, relying inertia. This is where your rotating mass (includes the flywheel) comes into play. The store energy is released. At lower RPM, more energy is released. There is more time for it to be used. At high RPM, less energy is released. A large flywheel requires a lot of energy to move, in turn, it stores a lot. If your running through the trails, and hit thick mud, the stored energy has even more time to be used, helping the motor stay alive... Now the flipside. At high RPM, it takes exponentially more energy to get the heavy flywheel spinning. Shave off a bunch of weight and pretend you have a 2 inch flywheel(pvl, hpi, yz125), and it can rev very quickly, and maintain power, but only in the powerband. The energy required to spin the flywheel is very small. The amount of stored energy only is just enough between power strokes at 10k RPM. Thick mud would be problematic if you're outside the powerband. There is a balancing act here. A 1000 gram flywheel that is about 100-105mm in diameter and 25-28mm thick is a great set up for the 125. Drag racing would be much smaller. There are many flywheel options out there that we don't speak about.
The pipe. .... This needs to go in another post.
Sorry for the delay, Theres a lot of information and it takes time to try and get it all into a single post on a phone.