In trying to convert Rise of the Runelords for an upcoming 5th edition game. Monsters I'm simply going to swap out with the equivalents in the Monster Manual, but are there any guides for converting the campaigns custom NPC's?
Refer to the DMG.
Chapter 4 of the DMG has lots of tables and advice for creating NPCs both as party followers and and villains.
Focus on fidelity of character and power level over slavish devotion to matching details.
Statistical and racial bonuses are going to be very different between the two. You should aim to keep the power level of the NPCs roughly the same in comparison to the party vs. trying to exactly emulate the spells and magic items the NPCs may or may not have had.
Use WOTC's own monsters as an example.
The Monster Manual has a lot of NPC spell casters and/or monsters that have strong innate abilities on par with spell casters. You may be simply able to reskin one of these or if not use them and their CR as a guideline for what should be level appropriate for the party.
Completely rebuild the character. Keep the character concept, and probably the class, race and level, but everything else will have to be redone from scratch. I know this isn't likely what you want to hear, but Pathfinder and 5e are just too different of games for any meaningful conversion that preserves much more than that, because this is already pushing the limits of what post-3.x D&D preserves from its 3.x roots, which are its most recent common ancestor with Pathfinder.