shadow said:
1. Spells: 3.5e changed almost all the spells. Many spells changed levels making it difficult to convert spell casting characters
This is tough. If you have really many spellcasting NPCs, it could become a burden. Anyway, if you are the DM, remember that you should not let the players read the NPC statistics: this gives you the chance of not fully convert an NPC (or make mistakes

) without them noticing. I don't think there are spells changed of more than 1 level, and even those are not so many, but if the NPC casts a spell at a "wrong" level, how are the players going to notice, if they don't even know what is the NPC class level?
shadow said:
2. Monsters - specifically, monsters with DR. DR was changed in 3.5e, and I'm not really sure how to deal with it. Moreover, since 3.5e monsters are on average tougher than their 3e counterparts, how do I adjust DC?
The rules-of-thumb suggested can help you with this. If the 3.5 monster has DR X/Magic, then it is simply converted to X/+1.
As a simpler but rough option, you may consider to simply increase by 5/+1 the final DR for every alignment required to bypass it and by 5/+2 for every special material (which is harder to get), such as changing DR 10/Magic & Evil & Cold Iron into DR 20/+4 (+1 for Magic, another +1 for Evil, another +2 for Cold Iron).
shadow said:
3. Class abilities and skills - since a number of skills have been folded into Survival, what do I do to characters and PrCs that have ranks in the Survival skill. Also what about classes? Many of the classes have changed significantly. (Especially the ranger) This makes conversion somewhat of a problem with many classes. A 5th level ranger in 3.5e is completely different from a 5th level ranger in 3e in terms of power, skills, and abilities.
Skills shouldn't be a problem: whenever a Survival rank is required you just substitute Wilderness Lore; if a bonus is given to Survival, you may give it to Intuit Direction as well as Wilderness Lore. It is more difficult to adapt 3.0 skills to 3.5 that the other way around, IMHO.
Classes are a different thing: the 3.5 versions always have something more, and to take it away is more difficult than to add something. Just as an example, almost every class has more class skills and a couple of classes also have more skill points, therefore a written NPC may have higher ranks in something when he wouldn't have in 3.0, and if there are synergy bonuses it becomes a pain to change it back. But the point is... is it worth to convert every detail? How is a single extra skill of an NPC going to affect the game?
Class features are quite modular and shouldn't pose a serious threat if they moved up or down a class level. You may simply want to check by class, but it won't be hard. Rangers are of course completely different, and in that only case it could be easier to rewrite the NPC from scratch. If you anyway use custom classes or feats from non-core sources, you could even simply keep an NPC Ranger in his 3.5 form without expecting complaints from your audience.