Y33TREKker, I think you are definitely pointing in the right direction. I noticed that during heavy rains, I do get some water in somewhere behind the glove compartment - exactly where you said the harness is. Sometimes I can see the water running down to the floor from there.
Also, is it possible to get a copy of the '99 VX electrical manual that you have? The CD that I have is for 2000/01 VX which does have some differences - I noticed it when I was doing my start button mod. I am pretty sure I can still figure it out but if I could get a copy that would be great! Let me know please.
Thanks!
- Yefim