replaced the alternator and it starts fine.
Except there's now a transmission warning light.
The owners manual says this might go away on its on otherwise it will only work in forward gears only.
I will try it when I get home.
Also the key needs to be resynced AGAIN haha

The car starts fine so the battery is being charged.
BUT the transmission warning light wont go out.
I drove it for 5 minutes and the auto gear change is very clunky, particularly when coming to a stop, there's a major jolt at the back axle.
The key will not sync either.
The transmission works in reverse (according to bentley it shouldn't when in safety mode).

How can changing the alternator affect the transmission?

I spoke to the guy who replaced the alternator and he said when he moved the power steering reservoir he found a tube (air or vacuum) that was not connected to anything so when he replaced everything he left it unconnected as he assumed it was some sort of air sensor. Any idea what this tube might be from? The guy said he looked for somewhere to connect it to but couldn't find anything. It was sticking up behind the power steering reservoir.
Could moving the power steering reservoir affect the transmission?

There are several breathing tubes (vent pipes) that are unattached around the e53.

The one visible in the engine bay and is one of the most asked questions by new e53 owners...is the vent pipe for the front final drive:

The one on my car looks much thinner, maybe 1/4inch 3/8 wide

Take a look at this post over on BimFest's e53 forum...about a week and a half ago...a poster there also questioned what the unattached vent pipe was for on his 2001 X5 3.0 and posted pics of the tube/pipe: Bimmerfest - BMW Forums - View Single Post - Misterious vaccum line under the hood

Click the link above to see if that is the same part you're referring to on your 3.0.

Take a look at this post over on BimFest's e53 forum...about a week and a half ago...a poster there also questioned what the unattached vent pipe was for on his 2001 X5 3.0 and posted pics of the tube/pipe: Bimmerfest - BMW Forums - View Single Post - Misterious vaccum line under the hood

Click the link above to see if that is the same part you're referring to on your 3.0. And if all else fails...look for the BMW 11 digit (full) part nbr...or the 7 digit (partial nbr) that is usually printed on parts...then you can look it up on one of the online part sites (like the links provided above with the diagrams).

yep that looks like it, got that big bend in it.
I went through all of the underhood pics on bimmerfest and it didn't show up. I will have to give it another try. Thank You Qsilver7