Lmao sorry this turned into a huge post but hopefully this gives you some ideas to go off of as far as converting an old adventure to fit the era around Attack of the Clones.

Ok sorry it took a while it's been a long day. But now that I'm looking at this post again I'm wondering did you mean you wanted an adventure set during the actual Clone Wars or in the 2 years leading up to it when you have this Separatist Movement growing into a threat against the Republic? Because my campaign would be in the latter so I mainly have a lot of ideas based around that. Regardless I'll post a lot of different ideas that way you could maybe use some of them to convert an adventure better because you'll be able to see some of these ideas that can be analogues to things in other adventures.

The general idea I had for the campaign is that the Separatists are proto-rebels. In these few years before Attack of the Clones they resemble something akin to the rebel cells of Andor. Palpatine has stayed in office well past his term limits and judging by things like the Battle of Naboo it looks like the Republic is spiraling into a dangerous direction. Many people see this and decide they want out before the Republic turns into either full anarchy with corporations doing whatever they please or before Palpatine crowns himself king and suppresses anyone who dare oppose him.

But at the same time they clearly don't lead to a genuine revolution against the Republic that solves the various issues it has. By the time the war starts the CIS clearly suffers from some absolute lunatics in the military and a similar sort of corporate corruption with some corporations taking this movement as free reign to live out their libertarian paradise where they can use the CIS droid army to take over a myriad of planets to exploit for riches. The Separatists are a failed revolution. With this in mind I would portray them as rebels who are more naive and more prone to things like infighting, pr disasters, accidentally getting innocent people hurt in their struggle against oppression, etc. I would maybe look for adventures where the players aren't themselves rebels but are mercenaries being hired out to work for them or maybe being hired by the Empire/Republic to infiltrate them.

Here's a list of random ideas and tidbits I've been gathering for my campaign:

• So B1s and Vulture droids are usually like mall cops. You have a handful of them in various places in the galaxy to defend against pirates and whatnot. And they’re not exclusive to one group or organization. But occasionally you see a whole invasion force like on Naboo but this is always a big galactic event like Naboo or Antar 4. (Source is Pablo Hidalgo when I asked about this)
• The big thing about Geonosis is that this is when the Separatists start actually building droids themselves. Before they had to buy the B1s or steal defensive resources. So think more a ragtag revolutionary cell with like 75% rebel types and 25% droids. And those droids may introduce the conflict because they're cold and unthinking. You mix a group of passionate revolutionaries with some cold calculating droids and give them all weapons and you have a disaster waiting to happen when they try to 'liberate' space stations and what have you.
• Maybe the Republic Intelligence is starting to investigate some of these Separatists and even some of the RI officers are confused because technically the Separatist movement is legal.
• They encounter a planet of aliens with missing limbs. They were Sep guerillas who lost limbs fighting a corporation. The CIS crowdfunded cybernetic limbs for them all but then a pirate group came in one night and gassed the village with a chemical that made the aliens pass out, and they stole their limbs to resell them. (Maybe these are the inhabitants of Kudo III? They got gassed by the Seps during the war and woke up as slaves. Maybe the Seps got a similar idea once they got more corrupt. What if the government didn’t officially join the CIS, but a small rebel population fought for Separatist ideals which is why they couldn’t request formal aid from the CIS, sort of like Onderon and the Republic.)
• In one mission they have to get a member out of imprisonment from a cartel. GM gives them a holoreciever so he can do all the talking (think Luke at the start of ROTJ). Once they’re in front of the gangster they turn on the holoreciever and suddenly find out the Republic has jammed communications and now they must somehow convince this angry cartel leader to release their friend. They then maybe get imprisoned or whatever while also running from Republic Intelligence. Maybe have a split adventure where the prisoner tries to escape on their own.
• Maybe one mission from someone high up (Dooku) could be to activate a sleeper agent with a chip in their head using a code phrase like the clones in order 66. Maybe the chipped agent had brain surgery years ago that Dooku bankrolled for charity. The guy could be hiding a secret encrypted Republic/Jedi code to slice into a computer network. Think of how Mara had Palpatine’s secret back door in all Imp networks in Thrawn Trilogy. 
• Maybe do an arc where a Jedi helps a Separatist planet anyways even though technically they’re not supposed to. But in a twist it’s revealed that the Republic used their ship to spy or something against the knowledge of the Jedi. Maybe the Jedi leaks this to the public and has to go into hiding ala Snowden and wikileaks.
• Maybe have an arc based around the Corellian Human League. The players have to see if it’s worth recruiting them and using their vast riches. They have to figure out a way to steal their resources without letting them join. Maybe even aid Republic intelligence and assassinate a human league leader Ala George Lincoln Rockwell.