The papers, spanning 40-plus years and published online for the first time on Tuesday, reveal the difficulties of bedding in the new Doctor.
And internal memos show how his first transformation was originally envisaged as a bad LSD trip.
The Doctor first changed physically in 1966 when William Hartnell handed over to Patrick Troughton. "Once a brilliant but eccentric scientist, he now comes over as a half-witted clown," said one viewer of Troughton's new role.
In an internal memo dating from that year, producers said of the transformation: "It is as if he has had the L.S.D. drug and instead of experiencing the kicks, he has the hell and dank horror which can be its effect," the memo says.
The debut of Tom Baker - who went on to become one of the most popular incarnations - also drew much criticism. "General opinion was that the new Dr Who is a looney," said one viewer.
Roly Keating, the BBC's director for archive content, said: "As we welcome Matt Smith and Karen Gillan into the Tardis, it's the perfect moment to remember his predecessors and also to celebrate the work of the BBC Archive in preserving these documents and photographs for future generations."
The material will go online at bbc.co.uk/archive from Tuesday.