In regard to #3, are you using a cam that has decompression built in? If you have a cam with decompression, then the starter should be fine. Cams are important when going up in compression ratio, they let you use the power that is possible.
#1 I think this is always a good plan, these little machines work so very hard that a little extra cooling can't be a bad thing.
#2 I doubt this will be much of an effect, but I guess it is possible. And especially if you are running a wider gap on the plug. I would suggest a one number colder plug, maybe two colder because of the compression increase.
#4 are you using the stock head? People say the stock head is very poor with airflow. So if you are using the stock head, I doubt a larger throttle is going to do anything. That said, Mikuni rates the TM24 carb (24mm) at up to 20 horsepower. This leads me to think that there isn't much need to increase the throttle, intake, and port sizes much beyond 24mm. Would I try to smooth out any casting flaws in the stock head? Absolutely! Would I clean up the area around the valves (deshroud)? Again without question. Would I look for other areas where I could see obvious flow issues? Yes I would. And would I dimple the intake and port (and probably valve? Yes. In fact I have on my other small bike Final - Project 2 10/6/16 updated
and New carburetor and manifold/mount.
There are 3 parts of the new carb build, take a look around because there are other engine building tips like setting squish band.
After that you are into a race head, and I haven't found too many designed for the 125cc displacement.
And all this said, are you going to make HUGE power after all this? Well that depends on your definition of huge power. Will you see 1 or 2 horsepower increase? Maybe, and that is a huge percentage of the stock power.
Other things you will need: Fuel controller, exhaust, air filter or intake mod. Without doing these extra things, there will be no power to be gained.