Look at the charging circuit, what is the stator putting out? what is VR putting out? check your grounds, check wiring from VR back to battery, it may go through the key switch also. Plus check the PTO resistance in case that is having issues and drawing to much current. Most are around 4 ohms, anything less than 3.5 will starting draw to much current, don't get to worried till it is around 3 ohms.
/ John Deere 325 Garden tractor - Battery Charging Light
Welcome to TBN. Good advice above. When you are covering bases and cleaning terminals, clean the pigtail at the regulator extra good. Verifying system voltage would be a great idea with and without the PTO engaged.