Hello Corwyn77,
As one of the people who is working on converting this to PF for ENW (new thread on that soon!) I can honestly say that you will not be having that much of a problem.
Skill Checks: Spot/Listen goto Perception, Open Locks to disable Device, Acrobatics takes over everything but swim and climb. These are not that difficult.
Monsters: Most can be found on D20PFSRD (which I'm a contributor as well) and use them easily enough for ones that reference the Monster Manual. Any Big Monster you can run as is with adding a quick fix template to convert them on the fly (the location escapes me now).
NPCS: Here is where you have a choice. You can run them as is, and change a few hit points, and some feats around. Or convert them totally and make them equivalent to PF. There are several BBEG's and they very much deserve (and will get) a revamp using the APG/UM/UE guides that Paizo put out. You would be doing yourself a disservice if you didn't at least convert Leska over.
Pathfinder at high level is very similar to 3.x at high level. The battles are either going to be a cakewalk or a slugfest with lots of deaths. Don't feel bad if your party goes either way with these last 2 modules.