My Estimation of the Timeline Up Through the Beginning of Season 3
This first section has been pilfered from my own answer to another question:
Rick's group got to the farm maybe a month and a half after the outbreak started - maybe less - and left after only a few weeks (Lori wasn't visibly pregnant when they left).
Season 1 took place over the course of a few days (not including the shooting that put Rick in the hospital) - fewer days passed than there were episodes in the season; by my count, 5 days total, vs. 6 episodes.
Day 1: Rick wakes up and gets to Morgan's house, sleeps there. Day 2: Rick leaves Morgan at the police station, goes to Atlanta, meets Glenn and the others, and goes to their camp, where he finds his family; they all go to sleep. Day 3: Rick, Daryl, and T-Dog go to Atlanta to look for Merle, meet the Vatos, go back to camp after dark, and find it under attack; Amy and Jim are bitten, no one sleeps. Day 4: Amy and Jim die, the group goes to the CDC, gets drunk, then showers, Shane tries to rape Lori, everyone goes to sleep. Day 5: The group escapes the CDC, Jacqui dies in the explosion, the group spends the night camping somewhere near Atlanta (the season 2 debut begins with Rick on a rooftop overlooking Atlanta the next morning, talking on his walkie-talkie).
Season 2 began the day after the escape from the CDC, and ended about a month later, maybe a bit less, maybe a bit more, but they were on the farm for no less than 2-3 weeks, no more than 6 weeks - enough time for Lori to realize she was preggers, but not enough time for Shane's hair to grow back (he shaved it off the first night they were there, which was two nights after they left the CDC).
And since Rick would have died of dehydration if his coma lasted more than a week or two after the hospital was abandoned, and the hospital was abandoned shortly after Rick got there (things went bad VERY quickly, and hospitals were the first places to fall because that is where everyone who was bitten went), Rick couldn't have been in the hospital for very long.
When Rick woke up, he had a bit of stubble, but not much - I'd guess about 2 weeks' worth by average beard-growth rates - and the lights and water were still on; so he can't have been in the hospital for more than a week or two after it fell, maybe 3 weeks total after he was shot. Finally, Shane and Lori only hooked up after the city fell, probably after they got to the quarry campsite; she probably wouldn't know she was pregnant for a month or so after conception (she'd notice she missed her period before morning sickness started happening). So they left the farm no more than 8 weeks after the outbreak began, possibly as little as 5 weeks, probably closer to 6 weeks.
By the time they reached the prison, Lori was very pregnant, and they had spent the entire winter on the road (they said so); it seemed very warm already, so it was probably mid-late spring; on the farm it seemed warm, but not terribly hot, and they were worried about it getting cold soon (the subject came up late in season 2). This suggests that they left the farm in early/mid fall (leaves were still on the trees and still green). So between the end of season 2 and the beginning of season 3, at least 4 months passed, possibly as much as 6 months. That is 4-6 months of survivors dying and coming back as zombies. 4-6 months of zombies leaving the abandoned cities and spreading slowly across the countryside. 4-6 months of zombies clumping into groups, groups merging into herds, and herds roaming around, sometimes aimlessly, sometimes chasing prey.
My Estimation of the Timeline of Chupacabra vs. the Timeline Suggested by Jenner's Statement
Chupacabra happens shortly after the group arrives on the farm, because the need to search for Sophia is still the top priority, and Carl's injury is still just beginning to heal.
However, this contradicts what Dr. Jenner at the CDC said in episode 5 of season 1:
It's day 194 since Wildfire was declared and 63 days since the disease abruptly went global.
I see no way to reconcile Jenner's statement with the events on the show, unless Rick was in the hospital for much longer than I believe. Rick was clearly surprised by what he found when he woke up, so he obviously didn't know anything about the outbreak when he was shot and went into a coma. As a first responder, he would presumably have been told at least something about the outbreak, had it been in progress at the time of his shooting.
So if Jenner is correct about the timeline, and if the show is telling us that he made this statement the day that the group arrived at the CDC, then Chupacabra takes place about 200 days after "wildfire was declared" (whatever that means) and about 70 days after "the disease abruptly went global".
If my estimation is correct, on the other hand, then Chupacabra takes place about six or seven weeks after the outbreak began.
The Timeline Provided by the Walking Dead Wiki
The TWD wiki's timeline says that Chupacabra takes place at least 69 days after the outbreak began.
The next day Lori wakes up and talks to Carol about using the farmhouse kitchen. Meanwhile the group is still searching for Sophia and Jimmy joins them. Shane decides that he will begin gun training the next day. (Chupacabra)
Shane questions Rick’s decision to keep searching for the girl. When they return Rick and Lori talk about continuing the search. Beth calls for Rick to talk to Hershel. Hershel is not happy about Jimmy joining the group and Daryl taking a horse. He and Rick agree to control their own people.(Chupacabra)
Daryl finds Sophia's doll in a riverbed. He continues to search but his horse throws him and he falls on one of his arrows. He has a vision of Merle and awakens to find a walker biting at his work boots. He dispatches that walker and another and then climbs out of the ravine. (Chupacabra)
Glenn and Dale talk about the women and Glenn admits he had sex with Maggie. Andrea thinks she sees a walker emerge from the woods. Rick and co. approach the person to discover it is Daryl. Andrea blinded by the sun shoots Daryl in the temple. Later Hershel tends to Daryl’s wounds as Dale comforts Andrea. At the supper table there is awkward silence as Maggie slips Glenn a note. Glenn returns the note. (Chupacabra)
That evening Maggie checks the note and realizes Glenn is in the barn. She runs to the barn to find Glenn has discovered a number of walkers. She tells him that "[he wasn't] supposed to see this" as the walkers push at the barn door. (Chupacabra)