Michael Langford-Johnston, 64, who retired from Strathclyde Police in 2001 with the rank of Detective Inspector after 32 years service, had faced a second day of questions about a teenager's story that the girl died during a group sex attack.
Colin McIntyre, 44, allegedly "confessed" to being at the scene - just yards from Ms Doyle'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 made up the contested statement.
The trial heard that in spite of Mr McIntyre's account of standing by while Ms Doyle, 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 was not charged with wasting police time.
Questions about what had happened to the string supposedly used to strangle Ms Doyle and another weapon were not asked.
After Mr Langford-Johnston's long session in the witness box, defence QC Donald Findlay suggested the investigation was a disgrace.
The lawyer said: "From what we have seen in this, I suggest this inquiry - in this area alone - never mind whatever else the ladies and gentlemen of the jury have heard - was shambolic, disgraceful, at least."
The former detective told him: "I would like to think I could have done a lot better."
Mr Findlay pressed: "Why on earth, 28 years down the road, should the ladies and gentlemen of the jury put any faith in that police inquiry?"
Mr Langford-Johnston replied: "That I cannot answer."
John Docherty, 49, now of Hunters' Quay, Holiday Village, Dunoon, denies murdering Ms Doyle, 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 into the murder.
The charge alleges that on June 2, 1986, in a lane near Elaine Doyle's home in Ardgowan Street, Greenock, he seized her by the hair, struck her on the head and either removed or compelled her to remove her clothing.
The charge goes on to allege that Docherty forced Ms Doyle to the ground, pushed her face into the ground, sat or knelt on the teenager then placed a ligature round her neck and strangled her.
Docherty also denies stealing a handbag from Ardgowan Street on the same date.
He further denies a charge of attacking another woman, Linda Hargie, on various occasions between 1990 and 1995 at an address in Anne Street, Greenock by seizing her and pushing her and punching her on the head.
The trial - which the jury have been told could last another six weeks - continues.