Oh Speedy!
To be so young and dumb and full of energy! I've been through ALL the same thoughts and desires. Nothing wrong with that. But for you to do what you wish you still need LOTS more than desire and an engineering degree. MTK is mostly right, but you have a chance of success. You can learn from this and perhaps end up with a ridable bike. You don't appear to want advice, you've written off the logical machines. The KDX series engines could be made killer and their chassis are better than aluminum. For you to do more than design a cylinder for a CR125, to actually make patterns and cores for ports, fabricate/adapt power-valve pieces and finish a cylinder and head so the transfer flow worked for adequate power, would be a miracle. Don't give up on making something better, just don't try to reinvent the wheel. Get a 1990-1999 or 2005-2007 CR125, bore and stroke it to 155/165. It could scream if it was done/ported right. It might not be so reliable. The YZ125 would also work.
I hate to rain on your parade, but I've been there. I built a 168 lb 250 Montesa powered bike as one college engineering project in 1976. I disturbed classes in the ME building with a Suzuki TM 125 engine on the dyno doing durability testing for exhaust port shape/ring wear. I made patterns and molds for casting reed cages and manifolds as a student. I was lucky enough to work at an aerospace machine shop from age 16. That gave me some of the skills and equipment to build my dream machimes/parts. Don't give up the desire to create, just walk before you run. Make a big bore 125. Try it wthout power-valves with a low exhaust port. Try the exhaust port higher. Bring the transfers up gradually. See what these things do to your powerband. Make a cast head first. Get used to what happens to aluminum when it is liquid poured into a mold. Learn. Then go to the next step, the cylinder...