The result was an average wait of 90 minutes in October at San Ysidro, with vehicles usually waiting half an hour more.
Those waits translate into many millions of lost dollars in commerce on both sides of the border, as few shoppers from either nation now bother.
Delays are not as long at some other border crossings, where traffic is not as heavy. But the INS says the peak wait for people crossing from Mexicali into Calexico nevertheless has reached about 55 minutes.
Those waits wreak havoc on merchants on both sides of the border and their employees. With cross-border traffic down by about 30 percent from last year's levels, so are sales at stores on both sides of the border. Shops on both sides of the border often sit forlorn, with clerks who haven't already been laid off frequently reduced to strumming guitars as they pass the time.
Business is so bad that Democratic Congressman Bob Filner of San Diego asked President Bush to declare a state of emergency along the entire Southwest border.
Filner supports tight security, but wants the federal government to bring in more inspectors to keep traffic moving.
"Let's do everything we need to keep terrorists out, but let's provide the resources to make sure our economy doesn't die in the San Diego area," he said.
The rest of California is afflicted, too, as hundreds of trucks carrying this state's exports south sit for hours every day on their return trips.
The INS claims border waits could be cut substantially if more people who cross carried photo identification such as passports, green cards and drivers licenses that can be easily checked by the IBIS system.
"Threat Level 1 means we have to do 100 percent checks of all pedestrians and virtually everyone in every vehicle," said spokesman Virginia Kice. "The waiting times are starting to come down as people become aware that bringing the right documents can speed things up."
The INS reports processing times for persons without photo IDs average about two minutes, as they are asked several questions, while persons with scannable documents can get through in as little as 15 seconds.
The immigration service also says it's well aware of the economic disruption caused by heightened security.
"We're trying to address these more intensive inspections with all the resources at our disposal," said another INS spokeswoman, Kimberly Weissman. "We're also looking into new technology."
The most likely improvement: Deployment of many more INSpass machines. These devices, now used by frequent international travelers at the San Francisco and Los Angeles airports and six others around the nation, allow registered and background-checked inbound passengers to insert a card and place a hand on a screen to verify their identity via hand biometrics.
"That takes only about 15 seconds, and we're now reviewing where we can put more of them," said Weissman.
Travelers can apply to join the INSpass system at airports where it is in use, but not yet at the border.
Modernization may be too slow to save many merchants. Revenues are down 40 percent at many stores in southern San Diego County. Merchants on Tijuana's normally crowded Avenida Revolucion report sales were off 72 percent in September from last year.
"Ever since this happened, no one comes," said Hernando Fuentes, who has operated a kiosk on the street for 20 years.
He and his fellow border-area merchants, plus many others who export to Mexico, are victims of the law of unintended consequences, which guaranteed that someone other than Osama bin Laden or his intended targets would also get hurt.