There are 2 things that I can think of. First, check that the rubber bond has not failed on the crank pulley. This is not uncommon, and will lead to the Alt not charging, or charging intermittantly. Chasing this can make you crazy!. The inside part will turn at engine speed, and the outer will turn much slower. Since the other belts are driven off of bolt on pulleys, nothing else will be affected. The second thing is the "dump module" I cannot remember if they kept it after the XJ40s, but if they did, it is a small black box with a small wire that connects to a stud on the alternator. This is not to be confused to the heavy power wire. If it has a dump module, you can disconnect it and run the car. If it is bad, the car will charge normally. Replace it, do not leave it off forever, it is there for a reason. HTH
Jesse