Michael Langford-Johnston, 64, who retired from Strathclyde Police in 2001 with the rank of detective inspector after 32 years service, faced a second day of questions about a teenager's story that the girl died during a sex attack.
Colin McIntyre, 44, allegedly "confessed" to being at the scene - just yards from Elaine's Greenock home - when she was stripped and strangled.
Mr Langford-Johnston denied that Mr McIntyre, then 16, was bullied or that he and his colleague had made up the contested statement.
The trial heard that in spite of Mr McIntyre's account of standing by while Elaine, 16, died at the hands of another youth, none of the "gang" was charged.
An alibi, which Mr McIntyre had given earlier, checked out but he wasn't charged with wasting police time.
Questions about what had happened to string supposedly used to strangle Elaine - and another weapon - were not asked.
During Mr Langford-Johnston's long session in the witness box, Donald Findlay QC, defending suggested the investig-ation was a disgrace.
The lawyer said: "From what we have seen in this, I suggest this inquiry - in this area alone - was shambolic, disgraceful, at least."
"I would like to think I could have done a lot better," the former detective told him.
Mr Findlay pressed: "Why on earth, 28 years down the road, should the jury put any faith in that police inquiry?" Mr Langford-Johnston replied: "That I cannot answer."
John Docherty, 49, of Dunoon, denies murdering Elaine, claiming he was with his parents - who are no longer alive - at their home in Anne Street.
Docherty has also lodged a so-called special defence of incrimination claiming the culprit might be among a list of 41 names taken from files of the police investigation.
The charge alleges that on June 2 1986 in a lane near Elaine's home he seized her by the hair, struck her on the head and removed or compelled her to remove her clothing.