We are planning on heading into Bolivia from San Pedro de Atacama, Chile. Would appreciate feedback from anyone who has made the trip regarding best route, transport and border crossing. Plus any scams!

I didn´t do that crossing myself but I met a few people that did. It´s really easy if you book a 3 day tour to Uyuni, for about 65 to 75 US Dollars. The first day is a lot of driving and the border crossing. Day 2 is to see the lagunas, Geisers, volcanoes and Flamingos. Day 3 is about seeing the Salt Flats. The tour will end in Uyuni.

The scenery in this part of Bolivia really is stunning.

I´ve recently done the tour from San Pedro to Uyuni,

I was with a company called Estrellas de Sur based in San Pedro and the 3 day 2 night tour cost 85 dollars. A few companies offer the tour from San Pedro but I had this one recommended and the tour went without problems.
I´ve heard stories about some drivers being drunk or there being lots of breakdowns. Just watch out for anywhere offering suspiciously low prices.

The scenery is indeed stunning. In fact it was so stunning that I´d say the 85 dollars is the best money I´ve ever spent on my travels.
Make sure your camera battery is charged and that you´ve got lots of memory/film.