Welcome to the site !!
It sounds like you replaced the Needle , but not the Needle Jet , that is the long tube the Main Jet goes in and sticks up thru into the venturi , if the Needle itself had any signs of wear (the old one) , then it most likely ovaled out the Needle Jet , and that allows the Needle to kind of bounce around , allowing it to sort of seal , then allow fuel passage in the worn out area , so what the bike does is surge fuel when its in the sloppy part of the tube , so you get RPM changes as fuel is increased , then restricted .... make sense ??
Replace the Needle Jet and you should be good with that , i would also replace the Floating Valve Seal , it is the O-Ring looking thing on the plate that comes off the slide , if its bad it can also cause erratic idle issues , make sure when removing it , to note the orientation of the Floating Valve Plate , it needs to go back together "exactly" as it came out ...... As far as the header glowing , they do glow anyways when the engine is run as they are around 1500 degrees when at a idle , if you ran the bike at night in the dark you would be amazed at how red the header gets , and its made worse when your just sitting there running without any airflow helping cool the header .... with that said , i would replace the Pilot with a #45 instead of the #42 , its too lean on the bottom end from the factory and keeping the smaller pilot makes you fight tuning , but its too rich on the top end , so you need to drop the main jet size also go make it run better . i run a 45/160 at 2000 ft
Here is a Jetting Guide made up by the resident carb guru here ... (Leardriver) , run what it says and you should be good
Jetting Guide for Main Jet:(pilot 45) CRF450R/X
One main jet size (up/down) for every 2,000 feet or 25 degrees in temp.