Monsters in 3.5 should have their CR reduced, and you'll need to calculate CMB/CMD for them.
For classes, I haven't had that issue as my group stuck to the pathfinder classes after we switched. It does mean we lose out on some of the 3.5 classes, like Warlock or Artificer, but we get by.
Overall, PC classes are a bit more powerful, but many of the "problem" spells were split up/significantly weakened.
The biggest difference between 3.5 and Pathfinder is the use of archetypes (similar to racial substitution levels, but more focused on general themes) instead of prestige classes to "personalize" a character. Also, base classes are normally more attractive than prestige classes for advancement; unlike 3.5, Pathfinder doesn't require a character to take levels in at least two or three prestige classes to "stay relevant."
Many of the 3.5 alternate classes have Pathfinder equivalents (you may have to stretch a bit or go by concept more than exact system mechanics). Artificer is one that is problematic (from a balance standpoint and there being no one single equivalent; depending on the exact concept, you could be looking at a gunslinger/alchemist, a magus/technomancer, a synthesist summoner, or something else), but the Pathfinder "warlock" is the kineticist (Occult Adventures).
Pathfinder races are more powerful and a number of well thought out 3pp ones exist.
A number of problem rules are dealt with and I use a Rules Lawyer to deal with them.