So, I've played lots of 3.5 and Pathfinder over the years, but haven't run any. I'd have preferred to run an AP for my regular group, but other folks in it are regular PF GMs and thus have all of the APs.
But I have my copy of the Freeport Trilogy that I got from backing the kickstarter, and I'm taking a swing at converting it. Sadly, my google-fu did not find that someone had already done the work for me, but I'm willing to take a swing at it.
The encounters are listed as EL X. If I'm reading this right, if an encounter is EL (X) in 3.5, it's equivalent to an encounter of CR (X+1) for a Pathfinder group of 4 PCs.
So, the first encounter is listed as EL 4 (a group of 8 Level 2 Experts). To make an equivalently difficult challenge, I should create an encounter of CR 5.
That's a budget of 1,600 XP. So using the the Shipmate from the NPC Codex (Warrior 1/Expert 1 - CR 1/2, 200 XP), I should use 8 of them.
Bonus Question: I'll have 6 PCs, so I should really bump the CR by +1 to 6, which means a budget of 2,400, or 12 Shipmates.
That said, an CR 5 encounter struck me as a bit harsh for a group of 4 1st level PCs, but then I read the tactics and saw they they'll bug out after 3 of them have died, so the encounter isn't really as tough as that.