Yes, that was the year with Michael the murderer and Jennifer Bransford, which was almost certainly a JFP power move IMO - she had been fairly marginalized once Guza returned, and most creative control was given to him. From what I understand she influenced stories and casting where she could, generally with lesser players. Tamara Braun quit because she was sick of Sonny, Jason and the mob. The Bransford casting imploded fast. Kari Wuhrer was embarrassingly bad as Reese. The Michael story met huge backlash and they hastily did a rewrite involving Michael's doctor, old footage of Billy Warlock from years past, and the outrageous claim that the doctor had been hired by A.J. to kill Jason in his coma in the '90s. This was also the summer of the terrible dancing doppleganger story (because Kelly Monaco had just joined DWTS) with Sam and Meg Bennett and her Sam-lookalike daughter, and Michael hallucinating an imaginary friend, "Jodie" who he talked to in front of other people. TPTB claimed this was their reward to Dylan Cash for being an "amazing" young actor. It did not go well.
The Alexis/Sam/Ric stuff was the following year. I believe the Ric thing began as KM began making noise about leaving - so they turned Sam into a villainess for a year or two (her most compelling period, IMO).
Emily was raped by Nik's doppleganger in late 04-early 05. Emily had difficulty being with Nikolas after that because of the rape, and gravitated towards spending time with Michael and Morgan at Sonny's house. Nikolas and Courtney was the summer of 2005, and wow was it bad. Guza obviously did not give a [!@#$%^&*] about either of them, that much was clear, but the actors had allegedly been pushing for it. They were B/C characters to him at that point without Frons' continued attention to Alicia Leigh Willis. Guza could be vindictive and the story seemed designed to make them hurt, because the writing drove the characters into the ground. Guza had never had much use for Courtney and iced her the following winter after she spent months offscreen. The affair also ushered in Sonny and Emily; Emily had been caring for the boys with Carly ill - she was basically the nanny - and went to stay with them at Sonny's when she learned of Nik's affair. I saw Sonny/Emily coming very early, like a train wreck. People called me crazy, yet I still could not believe my eyes as it progressed. It was (mercifully) over by the fall of '06, IIRC.
They did change some things for the better with the revamp: Laura Wright came in strong and nabbed a surprisingly good (if very sudden) pairing with Jax on the B-list, Robin and Patrick ushered in a considerable new re-focus on the hospital and characters in it, and Robert and Anna began to recur in '06. Robin also became central again despite continued attempts to demean her. I would never call it a great show in those years and mostly ceased regularly watching for years on end around that point until 2012, but Guza's awful second reign was never worse than 2005 for me.
On a side note, during the writer's strike a few years later, JFP re-masterminded Claudia's introduction (which Guza had planned separately but was not present to execute) and botched it as well - some sort of color-coded thematic thing similar to the failed rollout of Angel in 2001, and to some work I believe she did at GL, maybe with Tangie Hill. With Guza out of the building she also tried to launch a massive story with Ric and his newbie immigrant wife, all of which fans hated.