The D3 Tech Dump thread is your friend here.

Group 60 in the following PDF from that thread:

28-Service Manual General body repairs exterior.pdf

The replacement roof is now in and working. Here is the procedure I used, with reference to the manual helpfully provided above.

I had contravened the manual by removing the motor from the broken roof in the open position, simply because the roof was stiff and in danger of damaging the motor if I tried to close it. So, with the motor in my hand I reconnected it to the car and turned the switch to closed. The motor whirred to closed and stopped, at which point I disconnected it and popped the plastic cover off the alignment inspection point on the main motor. At that point the manual suggests to line up the yellow dot with the centre and the dot on the other side. It was interesting that I did have to adjust it by turning the gear with a pair of grips, in order to line it up. I estimate that I moved it one or two teeth. I don’t know if this was because I had removed it in the open position or because of the faults that had developed on my original roof, but for sure it did need adjustment. I then replaced the plastic cover and mounted the motor to the replacement roof (which remember was in the closed position.)

I then carefully cleaned the sliders on the half of the roof accessible with it closed, and lubricated them with the G00045002 Audi/VW grease which I’d bought - about £40(!). I then switched the car on with the roof switch connected and the loom passed out of the car to the roof propped up on its side. I set the roof to open and it duly slid back. I repeated the clean on grease on the other half.

I then installed the front deflector motor (I had bought a brand new one as the old one was grinding and from what I can see it’s a very common issue so I didn’t fancy a used one.) Remember you can only install the front motor when the roof is open, the inverse of the main motor. This done I refitted the front deflector.

For the re installation I had two helpers, seats down and some towels to protect them. It’s helpful to have some duct tape and put two or three layers on the hinge edge of the rear door interior panel and also the paintwork on the door jamb, because the roof comes very, very close on reinstallation. The technique we used was one guy in the drivers area facing back who receives the roof from another guy posting the roof in the passenger rear door. The third person watches the clearance on the trim and has nuts ready to screw on. Once the roof is inside it’s just up onto the mounts and bolt in, making sure not to trap the loom on the passenger front side as it’s very close to the sunroof tray.

Setup then was just ignition on, turn the roof to closed (holding my breath!) - it worked fine. Then, pull the tilt control and hold for five seconds to initialise the deflector motor (it responds with a little whirring noise) and then release and pull again quickly to run the setup on the main roof motor.

With those steps taken I now have a perfectly working and lubricated roof. I do have to reinstall the headlining still, but I don’t expect that to be worthy of writing anything.

Thanks for assistance on this and I hope my write up helps someone.

Good work! How difficult to remove the headlining without damage? One man or two man job and I guess it's possible with the seats in?

It’s a two man job really - I had one person in the back and one in the front, releasing the last bolts to lower down carefully. Front seats pushed back and reclined as far as possible.

It’s then quite tricky to get it out of the drivers side rear door - carefully adjusting position without scratching any trim.

I’d say it was two hours work to remove the headlining start to finish and another two hours to put it back. Certainly isn’t “a nightmare” and all the a b and c pillar trims come off and go back pretty nicely which is a refreshing change. You can tell the A8 is properly engineered with little things like that.