Awesome build!
I am new to mini bikes but was just kicking around building something up with a shifter setup rather than a clutch/CVT...Your build may have swayed me!
Of course the manual transmission adds different complexity aspects to the build as compared to a CVT. Foot peg positioning becomes pretty critical and I was concerned whether I would get it right. Since the clutch lever ends up on the left handle bar a foot brake really makes sense, but not to say that you couldn't put the brake lever on the right side handle bar. I often looked at motorcycle and minibike pictures to figure things out. In the end I had to modify my original pedal designs to make it work, but for me it was worth the extra work. I just like to shift, whether it is a bike or my own personal car.
I got a lot of help from members here, especially jdog, otherwise known as Jason. Unfortunately he had some personal concerns to take care of and I haven't seen him on this site for quite awhile now. I really miss him and expect others here do, too. His beautiful shifter bike build is certainly worth taking a look at. I looked at it countless times. If you build a shifter bike I would be happy to answer any questions that I could help you with. One of the big things Jason did for me was to mail me the template for the engine mount. If you need it, I could mail you a copy of it.
I had to search like hell to find a manual transmission 125cc engine with electric start that was available in the U.S. The Loncin that I bought has proven to be good so far and it starts up right away. By the way, if I did it over again I would consider using an 80-110cc engine. I like the power of the 125cc but it seems a bit of overkill. I assume the 125cc engine is bigger overall than the smaller engines and its size makes it just that much harder to fit everything within the frame. Before I bought a frame I did a lot of research regarding size and ended up buying one from Bad Dog in San Diego. They were good to deal with and worked with me to build the frame and forks as I wished; just bare bones with the engine mounting plate loose. Good luck, and I hope you have as much fun as I did!