Sounds to me like the stock CDI is not derestricted (not sure about 2012 A50 CDIs though, may come non-restricted) and the new 'racing' CDI is not compatible with an A50. Thus why the scoot doesn't reach over 38mph indicated and why the starter doesnt work with the new CDI. My A50 reached an indicated 45 with just derestricted stock CDI and derestricted boss. If your drive boss and jet are derestricted then this is what is holding you back.
Also when you derestrict a scoot you have to retune your CVT. You will probably want 5.5g roller weights along with a stronger torque spring (such as 1500rpm spring). If you read around through this forum this is what many people find to work as the best set up for a derestricted A50.
The stronger torque spring helps the scoot maintain speed uphill by raising the RPMs inside the powerband. The lighter 5.5g weights (stock 6.5g) helps the scooter accelerate much faster by keeping the RPMs higher right in the powerband of the scoot.
Read around this forum to see if the 2012 CDIs come restricted or unrestricted. Also this problem could be caused by clogged air filter or valves that are not at the correct valve clearance.
Also my A50 is a 2009. So i used this video:
Cutting Kymco Agility 50cc CDIAgain I would make sure the CDI doesnt come unrestricted before doing this.