My table is currently on chapter 4 of Age of Worms, a 3.5 AP from Paizo. While Pathfinder obviously has things that are unique to itself, I would imagine it is fairly similar. My steps to converting this AP include:
1. Compile a list of all encounters for the chapter. Take note of the creatures involved and the Encounter Level Difficulty.
2. Choose monsters. Find as many creatures as possible from the Monster Manual that match creatures from the chapter. For the rest of the creatures, chose a creature that is reasonably close and modify any special traits to fit what the AP calls for. Finally, modify NPCs as necessary to match what are in the encounters.
3. Figure out encounter balance. For each encounter, determine the moderate encounter difficulty for your party if they were the level called for in the EL for the encounter regardless of the actual level of your party. This will give a variety of encounters from deadly to easy.
4. Determine treasure and magical items. APs determine what the treasure will be, so find the 5e version of what you will be handing out or make up an appropriate 5e version. This will be much easier when the DMG comes out in a month. I record all of these in a separate document.
5. Determine DCs of checks and saves. Reflex = Dex, Fortitude = Con, Will = Wis. Because abilities and skills scale so quickly in 3.5, these numbers often need to come down. This will be easier with the DMG, but in general using the following guideline will help. 5 = Trivial (don't bother), 10 = easy, 15 = moderate, 20 = Hard, 25 = Very Hard, 30 = Need some luck because a trained character with a +6 proficiency and 20 in the corresponding ability will need to roll a 19. In general, numbers will need to scale down by 5 or 10 or more as the AP progresses.
I have made myself a bestiary of the creatures in the AP as I come across them. I then copy and paste them into a second document that has the creatures for each encounter grouped together on a page along with how many there are supposed to be of each type. At the table, I have a binder full of these pages so I have everything I need creature-wise at my fingertips. I use my spell card generator to make spell cards for any magic using NPCs and insert the spell cards in a trading card binder sleeve so they are right next to the NPC and I don't have to search through my PHB. My laptop is open to the current place in the chapter.
This is definitely more work than running everything off the cuff. However, you generally know where the party is going, so you can prepare everything well in advance. I can't really give you a good time estimate because I also make scenery and paint minis, but I will be happy to answer any other questions you may have.