always seat the carbs with airbox detached. with B4 seating the airbox is quite easy (except of getting drain hose to be routed correctly) - compared to 1st gen B6. and if you can't seat it no matter of what you can suspect that the reason is that carbs are not being seated properly too.
Really? It was taking me around 20 mins to get the airbox on previously, even with refitting the carbs I found it quicker and easier to put the airbox on first. Now that I've done it once and know how far the carbs go into the rubbers, it'll take about 5 mins.
Carbs are now balanced, well better balanced than they were before. Engines sounding better and it'll rev right up to the redline.
It also turns out the rad fan is working, it was a loose connection from where a replacement fan was spliced into the loom.
Next job is get the refurbished calipers back on and she's good to go.