This is definately a party built more for city/wilderness adventuring than dungeon crawling. Unless you have very understanding players or something, I'd recommend not doing a whole lot of those, since, as you speculate, they won't keep pace with what a lot of the monsters are designed for.
Of course, you could be an inflexible rod of verisimlitude and tell them to figure out the ways to meet their challenges, but only do that if your group thinks it's a fun challenge and not just you being a jerk because they didn't play cookie-cutter charaters.
Puzzles and NPC interaction involving skill checks and spells over simple player acting and player logic should work wonders. Combat should play a role, and a pretty big one, but ensure that the PCs can always get away. Cramped corridoors are their enemies, rooftops, sprawling streets, open fields, etc. will give them an advantage. They certainly can cope with a lot of foes, but it involves confronting those foes on their own territory, not the foes'.
Some ideas:
Home Invasion: Someone in the government is actually a doppelganger, and is using their influential abiltiies to pull in other doppelgangers, and their aberration-allies. As the natural defenses of the town collapse, the PC's must become guerrilla fighters, dodging and skulking in shadows, knowing the terrain and using it for their own tactical advantage. The enemeis may be giant tanks or powerful, city-leveling wizards, but better speed and local knowledge should prevail against them. The main opposition is aberrations of various CR's, until the PC's manage to confront and challenge the power behind the doppelgangers....
This plays to the Ranger's strengths, and utilizes the mobility of the monk to its' best. The rogue plays a key element as the one who designs traps, outfits locks, and knows the neighborhood. The bard manages to work against the doppelgangers and recruit help.
Foreign Lands: The PC's are used as sort of the Lewis and Clark of their day, exploring an empire recently annexxed onto the PC's main kingdom. There are locals there who don't recognize any sort of treaty that the PC's kingdoms may have signed, and the strange lands and strage creatures serve as the main challenges. The PC's must map out the world in front of them. To include the aberration angle, make the ruins of a vast empire prominent in this new region, complete with strange creatures that need to be exterminated for kingdom trading posts...or to earn the local's resepct.
This plays to the mobility of the monk and the adaptability of the rogue and ranger -- new territories and new creatures use their skills in new and interesting ways. The bard is satiated with diplomacy with local tribes, whom he can be instrumental as the first contact from the PC's kingdom.
Thieves! The PC's play as members or recruits of the local theives' guild. They make daring and highly publicised robberies, becoming celebreties in their own right. Stealthy and mobile, they can infiltrate even the most heavily-guarded of zones and swipe what their patrons require. A dragon's raid doesn't end with slaying the dragon, but in making off with the ancient crown the dragon holds. Perhaps they are even recruited by their own city's military to run raids against more insidious threats, or to help against the brewing war that is occuring. They make brilliant spies and scoundrels, and may have to break a few heads to get things done.
This plays to the fact that every class has Hide and Move Silently, and Listen and/or Spot as class skills. The adventure can run like Ocean's 11, or any other heist movie -- the rogue is the specialist who knows the area and the technology, the ranger is the expert marxman who can provide backup from a nearby rooftop, the monk is the mobile infiltrator whose speed means that no guard can catch them, and the bard is the front, who is able to get them the key at a nob's party while playing up a double-life.