Keep in mind that your group very likely has other means of travelling once they reach the part where they have to go to Jorgenfist, the Runeforge or Xin-Shalast. Teleportation, Transport via Plants, Wind Walk, Greater Teleportation... You don't really need modules or random encounters there.
However, for earlier parts of the AP, take a look at Chopper's Isle and The Lure of Greed from Wayfinder 7, Dawn of the Scarlet Sun if you want to expand on Magnimar, The Sanos Abduction fits into the voyage to Turtleback Ferry and there should be an adventure at the Storval Stairs that I'm unable to find right now that may be of interest if your group is short of XP before or after Jorgenfist
The first time I ran Runelords, I converted the 3.5 version while using the Medium advancement rate. I therefore had to add a fair amount of content.
I wrote a fair number of my own encounters and mini-adventures. The only one that I ended up self-publishing so far was "The Toadstool Goblins." (Note: I really need to go back and edit that adventure: I wrote it only a few months after I'd switched from 3.5 to Pathfinder, and it shows.)
Between Books 1 and 2, I added in "Chopper's Isle" from Wayfinder #7, and a modified version of Raging Swan's Dark Waters Rising set in Sandpoint (changing the ruins to have a Thassilonian theme).
Between Book 2 and 3, I ran a modified version of PFS Scenario #20, King Xeros of Old Azlant (changing the location to Magnimar and the name of the mysterious ghost ship to Emperor Xin). I also added Dawn of the Scarlet Sun during the events of Book 2.
Between Books 3 and 4, I wrote/cobbled together my own AP-length adventure "Seven Swords of Sin", to bring the number of books of the adventure to seven. The plot was: while the PCs were negotiating sales of Thassilonian artifacts recovered from Hook Mountain to the Pathfinder Society, the Aspis Consortium breaks into Heidmarch Manor to steal the fabled Sword of Lust from Heidmarch's private collection. Not wanting to bring in the Society, Heidmarch hires the PCs to track it down and return it. For that adventure, I strung together PFS Scenario 4-03 The Golemworks Incident, the riverboat journey from Magnimar to Kaer Maga from Pathfinder #63: The Asylum Stone (substituting in my own encounters involving a group of Aspis assassins), the jouney up the Halflight Path from PFS Scenario# 51 The Shadow Gambit, the intorduction to Kaer Maga from the module Seven Swords of Sin, the PFS scenario #4-10 Feast of Sigils, and a dungeon crawl that was an amalgamation of encounters from the Therassic Workshop area of The Asylum Stone and the dungeon of Seven Swords of Sin. In the end, as the dungeon collapsed around them, the PCs used a malfunctioning Thassilonian teleportation gate to the Devil's Platter near Sandpoint... where they fought the Sandpoint Devil.
Unfortunately, that campaign fell apart due to people moving out of town before we could pick Runelords proper back up again.
I had considered adding in Feast of Ravenmoor and Carnival of Tears at various points, but decided that they were designed for the wrong PC levels when they would have been most appropraite to use plot-wise.
I ended up not including it, but The Harrowing works great inserted at level 9, especially stories set in Varisia, and is a truly fantastic adventure.