The route from Keith to the Seaford Meadows site via Echunga, Meadows and Willunga Hill (the most direct route according to Google Maps - and I agree) is about 256 kilometres long. At 60 km/h that works out to just over four hours, for an earliest arrival some time after 7pm, nicely timed to avoid obstructing peak traffic.
I would be amazed if the overpass at McLaren Vale turned out to be any worse than any of the bridges on the South-Eastern Freeway, given it's a gold-plated monument to overengineering that was built over the main freight route to the south coast - a route which sees oversize loads on a regular basis. Even if it was a problem it would be easily dealt with by switching the route between Willunga Hill and Seaford to go across to Aldinga and north along the Old Coach Road - a route they may well choose anyway to reduce the number of roundabouts. Alternately, they could also avoid it by going from Meadows through Kangarilla and McLaren Flat instead of up to Willunga Hill.
I doubt there will be a long overnight stop anywhere, probably better to substitute a fresh crew and leave the first crew in a motel overnight to perform the same substitute duty the next day. That could well have happened already at somewhere like Bordertown.
Escorted oversize loads are not a problem at night, indeed it is often preferred to do it that way to minimise obstructions to the vast majority of people who don't give a rat's about new trains and just want to go about their daily business.