Welcome to the site !!
You did not mention replacing the Needle and Needle Jet , the Needle Jet is the long brass tube that holds the Main Jet and the Needle goes thru , when it and/or the needle wears out , it will oval out , your idle will be inconsistent and your bike will idle high , then the next time try to die or not idle at all , you adjust the idle and the bike is way too high , then drops back down without adjustment , you need to replace both the Needle and Needle Jet together , also , did you replace the Floating Valve Seal on the carb slide ?? , it can affect idle as well , you also did not mention the Accelerator Pump , it needs to be checked to make sure it's actually squirting and if so that it is timed correctly and is just barely missing the slide when the throttle is given (while the engine is off for testing , and the timing is set by a screw where the throttle cable wraps around the wheel on the carb under the black cover)
Overheating is usually caused by a lean condition , so even if the jets are clean or new does not guarantee they are correct for your elevation and temperatures your riding at , if the jets were what comes with it stock and you are not a Sea Level , then its not jetted correctly and will most likely be lean , which will also account for the hard starting since you have eliminated valves being out of spec , unfortunately , you might have to spend a little more , obviously the checking of the AP pump squirt can be done for free , but the rest of the parts will need to be replaced , but most are fairly inexpensive
This is the recommended jetting specs , if you're not within these specs , this could be part of your issue
Jetting Guide for Main Jet:(pilot 45) CRF450R/X
Sea level....165
2000 ft.......162
4000 ft.......160
6000 ft.......158
8000 ft.......155
Temperature/Elevation:
One main jet size (up/down) for every 2,000 feet or 25 degrees in temp.