Welcome,
So from 1999 up to and including 2003 you will get a BH5 twin turbo GTB Gen3. Later years will be the E Tune but not a lot difference. These are your twin turbo, sequential so like your old one wouldve been, primary turbo till around 4-4.5K then secondary until the world ends.
They can be mapped to around 315 bhp on standard engine by tuners like BR Developments. There is a home mod that you can do which I am literally just in the swings of trying now but waiting to get it on the rollers on Thursday to see if its safe.
Manual would be better for sure but people do seem to like the tiptronic, suppose this comes down to preference really. No issues with either as far as I know. Yes manual is more stock power 280bhp, 260bhp for the autos.
After the BH range you go to BP Twinscroll Gen4. This is a conventional single turbo set up. Twinscroll refers to the type of turbo. Sort of like having 2 turbos in one if you will. Much more efficient.
On stock mechanics you can get 320 bhp from them I believe.
In short, if you have the monies get a Twinscroll. A BH5 is lovely when it runs right but up keep is more key and they are sensitive. You will spend a lot more time fiddling