Al & Ed's Autosound said that they would not change the head unit in a post 98 A4 because it caused problems in the past. They said they had to pay $10k to Audi to settle a claim.
Perhaps they were referring to a car with the trip computer, which my car does not have.

Any thoughts would be greatly appreciated.

This may not be what you're looking for, but I wouldn't advise you to change out the head unit even if it wouldn't cause electrical problems. It is designed to fit and blend with the rest of the dash, and even the best after market units will stick out like a sore thumb. Why not just use the line level outputs at the head unit and run to a quality amplifier powering quality replacement speakers?

That's what I did, and the sound is fabulous. 1000% better than the stock or the flabby sounding (sorry, but it is!) Bose option, which I personally find unlistenable.

I have changed the head unit on my 99.5 A4Q. The only adverse effect that I have noticed is the loss of the radio/CD display on the computer panel.

However, unless you have a new head unit which can feed the rear active speakers and the front passive ones you will have to replace the rear speakers. I was so disappointed with the stock setup that I replaced everything - including cables.

The 99.5 uses a standard DIN space for the head unit but the stock unit is a little wider. You need to get little spacers (supplied by most car hi-fi shops). The result looks fine.

With my previous A4, a 96 model, it was easy to change just the head unit. With the latest model, you have to do a little more, but I think it is well worth it.