Time Spent Traveling
First of all, there are rules for overland movement that tell you how long it takes to move from place to place on a journey. This will tell you how long the travel takes, and should be accounted for in terms of events in the world and so on.
Describing the Journey
Prioritizing your game time, keeping decisions important and interruptions minimal
Secondly, yes, you should “skip” intervening details if nothing happens. Game time is always at a premium and should be spent playing. If the players stop for some reason (you tell them they saw something interesting, they just randomly decide to do something on their own, or they’re attacked), then you should also stop the “travel montage” and move into more finely described play, whether that be round-by-round for combat or just generally “real time” for finding an interesting ruin or whatever.
Otherwise, you should describe the road and the forests that they travel down and allow in-character time to greatly accelerate relative to realtime, to save game time for playing. If nothing has happened and the players have no reason to do anything but “continue walking down the trail,” then there’s no reason to waste game time asking them what they do. If they think of something they want to do (go hunt for herbs or game, whatever), they can tell you and then you can do that.
I have played games where the DM continually asks us what we do, except that we’re in nondescript terrain with no information that indicates we should do anything other than just continue, and it just comes off as an interruption. Worse still are things like “there’s a fork in the road, which way do you go?” “Do we know where each goes?” “No, you don’t,” “Well, how do each look?” “They look pretty much the same.” What purpose is there to this choice? Choices with no information are meaningless. So if you want to stop the party, make sure there’s something for them to actually do – randomly choosing is not really something to do. If knowing about that one path is better than the other requires skill checks (Survival, Knowledge, Spot, whatever), feel free to roll those for your players, and if they fail just flip a coin for which they go down.
Roleplaying! Don’t forget roleplaying.
The other thing to remember about journeys is that they are the times that allies become friends. Make sure you have your players roleplay out some of the conversation that takes place during the travel, and while a lot of that should be done in realtime, try to also get a sense of the topics that are covered during “fast-forward” time. How much do the characters reveal about themselves on the journey? Do we learn the city boy turns out to have an eye for birdwatching, that the hardened ranger has a particular distaste for certain foods? That kind of thing is really important to bringing a campaign alive. These things usually focus on the characters, not the environment. But also feel free to bring up aspects of the land they’re traveling through: a beautiful sunset, a majestic lake, a foreboding mountain in the distance, any kind of sight that would make even the most hurried travelers stop and look up. Find out how the characters react to these things. Just as the conversations they have give character to the team, the reactions to these sights give character to the world.
As for encounters that don’t buff them too much before the next dungeon, that’s a bit awkward. Weak encounters that pose no threat and offer no rewards are not typically worth stopping the party (stopping the game) for. You can very easily tell them about how they sent a bunch of meager bandits, poorly equipped and ill-trained, running after their ambush failed – and then the party can choose whether to chase them down to arrest or execute them or something, or let them run. But stopping the game for a fight that’s a foregone conclusion isn’t usually a good idea.
On the other hand, actually challenging the players, putting their resources or lives at risk, should have some form of reward, almost always XP and often gold or loot as well. That’s how the game works. If it’s happening too fast, the solution, more often than not, is to tell the players that you’re playing in a reduced-leveling-rate game, giving less XP in general so that they need more encounters to level up. But it’s important to be up-front about that. The other option is to go with more narrative leveling, i.e. you level up when you’ve done something grand and important and deserving of a new level. This often works better, but be careful about sapping player resources with no reward, or they’ll stop traveling.
Personally, I am not a fan of pre-made modules; I find they rarely are appropriate challenges for my party, even among my friends who think very little about optimization. For the most part they seem designed for the lowest denominator, and for a game as variable as 3.5, that can be very far short of a given party.
But, of course, there are also good reasons to use them; they greatly reduce the workload on the DM, which is crucial for those with busy real lives that must (sadly?) be prioritized ahead of gaming, but still want to game. So I understand the desire to use them.
There are two things I think you can take here, aside from simply redoing encounters at a new level.
Devise (if there isn’t a pre-made one) an arch-plot linking the plots together, and give the players strong incentive not to dally. Figure out, based on the distance between any two modules, how many encounters can be expected, and then try to choose your modules carefully so that the XP gained traveling from one to the next nicely lines the players up for what the next module expects. This, I suspect, is easier said than done, but it should be possible. Especially if you can count on the players taking the direct route (and they don’t think up some route more direct than you were expecting, of course) because of plot concerns.
When and if the players decide to go exploring/hunting more than you anticipated, at some point just swap the originally-planned-on-module for a different one. Maybe they reach their destination and find their quarries have already completed their goals and moved on, or maybe you can just find another module that’s set in the same area (or you can finesse the module into fitting that area). Effectively, the players have replaced the module with whatever wandering around the woods they elected to do.
In general, it probably makes sense to reward players for getting places quickly. Using random encounters to “farm” XP doesn’t make sense in a living world. If the players regret their delays, they’ll be more prompt in the future. And if the players manage to get to the next module more quickly (avoiding fights), that’s a good time to start subtracting from what the forces found there.
Travel Eventually Becomes Obsolete
In all cases, be aware that once higher levels become available, overland travel is probably going to stop being a thing. It will be replaced by flight, and then teleportation.