The starters look identical, but in fact they are different. everything you need for reverse lights, and to bypass the Park/Neutral Relay is on the TR connector, you don't have to connect the two wires to ground like what I did, they just need to be spliced together (cut and crimp?)
The 12v (green/black) from the TR switch should go to the reverse light switch, the other side should go to the blue/black wire on the TR Switch. Now if it's possible to make a harness (bad IP pump connector???) then that would make it very streightforward. there is not much for differences, and I never hooked up the clutch pedal.
The Axles are actually totally different in type, the manual ones are greased, and easily servicable, the auto ones are sealed at the transmission.
The mount is mostly different, I would get the whole thing just to be sure.
The hydraulic lines (don't forget the clips) Misc wires, connectors, etc...
All of the interior peices are the same, the only obvious difference is the boot and knob. You can remove this without taking apart the shifter, and it will drop right through the bottom of the car. (at least on my car) I got the whole interior console, but kept the original. since yours is the 6 speed, I would suggest the same.
So long as the 6 speed came from a TDI or other 4 cyl, you should be fine for the bellhousing, but you will notice that there are many different types, and some of the 6 speeds will have a higher RPM at cruise (the worst I found was like 3600 RPM @ 75 MPH). Swapping top gears in the 6 speed is also more difficult, but hey if you are autocrossing, then that should be fine on a short course. The diesel loves the tall gears... so I just stuck with the 5 speed... I would probably import one from a junker in europe so it would be cheaper... and have a better highway gear.
I would go inside your floorboard and make sure you have all of the things to hang the pedal from (there are three studs), and if they are not there (they are hidden under the fire retardent panel.), then you will have problems doing the swap... I haven't looked at many automatic golfs/jettas/passat/whatnots to see if they are the same or different. also it is quite obvious if your master cylinder reservour has a nipple available or not.
As for the brake pedal, all of the mk4 golfs I have seen, the automatic has the same pedal as the manual. if not, then that's yet another thing you would have to do that is not covered here...