So, my 98 Xj sport has the strangest problem to me. To start I was upgrading the factory speakers to some Terminator 6.5 speakers I purchased. All wired up and tried testing them, no sound from the driver door speaker. Ok so I googled what was wrong and found that the little wire in the door boot broke. Fixed that and tried again, still no sound from the driver door. Keep in mind I have the factory head unit with the little audio joystick. So again I tried fixing that wire thinking there was another break in it and removed the kick panel and rewired once again to no avail. I finally gave up and ran a wire directly from the head unit to the speaker. But this time when I tried I used the FM stations instead of the cassette aux player I have which I used the whole time and the speaker worked. But now my problem is the speakers work on the AM/FM setting but with the aux cord only the passenger side speaker works. How does that even make sense?

 

Sounds to me like one channel of your aux cord isn't working. OR the cassette unit amp is out on that channel. One night I was listening to the radio while doing my newspaper route and I was only getting one channel of their stereo broadcast, so I called them and asked them to check their output. This was when they actually had a live DJ on air late at night. He told me the signal was fine and I should check my receiver. Sure enough, I switched to another station and my left channel didn't get that either! D'oh! My radio was the problem! I actually called him back and apologized.

 

It sounds like your radio may be on the way out. Friend of mine had a similar issue with his 2000 XJ, and we did the same thing running new wiring direct from the stereo. He eventually caved and let me install an aftermarket head unit.
You can either find a factory replacement, or look into an aftermarket radio. You will probably get a little better sound in conjunction with the new speakers.