The oil was definitely too low for starters and it was probably running a little dry.
I did some reading online, modern gearboxes are incredibly sensitive to even minor discrepancies in oil level.
I've added about 350ml which is more than I thought it was going to need but I'm sure it's got the right amount now.
I'm really pleased with the end result, the gearbox is so incredibly smooth, the transformation is easily apparent.
I'm going to do the transfer case and rear differential as soon as possible. I need to go buy some thinner pipe however.
Audi say their gearboxes are a sealed system and don't need the oil changing but I would strongly recommend it anyway.
The oil I removed was awful and I doubt at 10 years, 114,000 miles it was doing even 1/5th the job it was doing originally.
I'm sure the transfer case will be just as bad when I go to do that too. I'm going to do my 184,000 mile Audi A4 next too, that's going to be fun.