I will answer the pacing problem first.
SPOILERS
I did have to give the party one push in the investigation. On their first day they followed the Dr. to the House of Blue Birds and stopped except to request information on Officier Porter. There was a half-hearted attempt to look for apothecaries. They also went to the Thinking Man's Tavern and the Parity Lake Police Department. These hints led them to Heward Sechim and then on to Nevard. The second day led them to the top of Cauldron Hill with a visit to the factory in the early hours of the third day. That morning they checked in at RHC HQ and then went to meet with Gale and before returning at noon to the RHC.
This is where I decided to push the party. According to the adventure as written, Nevard should have announced his plan to speak in Dawn Square on the forth. I decided to push out the announcement by a day so as not to conflict with the smuggling operation. I didn't want to force the party to decide which lead to follow or risk them splitting the party. So my push was to have Delft review what the players knew and then ask them to look into Sorhum and Starter to see what their involvement was. He also wanted to know what Recklinghausen took off the body. The constables took this cue to visit the Goodson Reformatory, which led them to the Wareyes. There they learned about the smuggling operation.
The constables debated long and hard about the smuggling operation. They felt it was irrelevant to the murder. In the end, they decided duty required them to investigate and maybe they might learn where the witch oil came from. With time to kill until the evening, they interviewed Camp and Kindleton. Kindleton agreed to try and meet with Recklinghausen and convince him to come in. She was going to try and establish contact on her own. The constables followed her in secret. I used this opportunity to have Kell's men kidnap her. Kell's me then brought the party in to the theater. They paid the ransom, were led to the church, drove off Creed, then snuck out the secret passage with Recklinghausen and Kindleton before Quital buried them alive. Quital murdered before the church. They still had enough time to return to the RHC and then head out to the baijou and make the exchange with the smugglers. So that was the end of day 4.
Day 5 saw them return to Flint in the early morning hours and report in at HQ. There they learned of the Dawn Square event later that day. Before heading off, one of the NPC's told them of the goings on in the warehouse district. They passed through Dawn Square on their way through and noted the gathering crowds. They fought their way into the warehouse and captured nearly all the technicians. They just had enough time to rush back to the square before Nevard's arrival. After rescuing Nevard, the returned to RHC with the evidence from the warehouse and requested an arrest warrant. They also really needed to recover.
Day 6 they headed off to confront Macbannin. They captured him and with his help, turned off the eldritch machine.