ORIGINAL: diablo_r
Happy reading, let me know what you think.
Wow, it was some reading

Good stuff. However I don't see clear conclusion tho. Let's bring the whole mod down to the pieces:
1. Compression increase by removing 0.4mm from the bottom of the cylinder. There is no really clear result of that - did or did not it improve engine performance. There is other issue not covered here: the engine was manufactured for low compression, so how does the increased compression impact on the bearings and rod. Both bearings are quite close together, so the force form the crank has big leverage on them.
And question how did you machine it? I mean the aluminum is not a big deal, but the liner is quite hard, isn't it?
2. Timing and port area. I also believe that this is the main restriction. I understood all the calculations (I mean the simply way) you put together so I have some idea where did you go. However again I have machining question. How did you open ports in the aluminum and cylinder liner.
As the final result is excellent with over 8500 rpm on 16x8 (is it APC or MA?) it's difficult to draw conclusion where is the source of that improvoement. I mean my engine turns 7400 now, - it is over 1k less but what I see there are four major elements that are different:
1. Exhaust. You are running kind of 'tuned' exhaust. This may mean a couple hundreds rpm more alone.
2. Carburator. I don't know if you changed it. I'm running stock Zama which is I believe 8mm venturi. Most 25cc conversion run 11mm venturi. It might be place to gain some power.
3. Compression. Mentioned before.
4. Port timing and size. Also clear explained by you.
I wish, we could compare the result on the same free-flowing exhaust (unrestrictive but not tuned) and the same carburator (I think maybe 11mm venturi) before and after the cutting the engine interior.
Thanks for the great info.
RysiuM
Edit: I just found: ZAMA C1U-W18 is 8mm venturi