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By Jennifer Friedlin, Associated Press

NEW YORK — Minas Polychronakis had a plan. In 1999, he renovated his shoe repair shop in the World Trade Center concourse. By 2004, the Greek native envisioned, he would sell his three-shop business and retire.

Then came Sept. 11.

"Now I have to figure out what I am going to do with the rest of my life," said Polychronakis, 61, a jar of 9-11 ashes perched on the near-empty shelves in one of his two remaining -- and struggling -- stores in lower Manhattan.

Small business owners downtown are still trying to get back on their feet after the Sept. 11 attack and an economic slowdown. An estimated 1,200 to 2,000 small businesses, including about 600 in the twin towers, have been wiped out, according to From the Ground Up, a small business advocacy group.

The federal government earmarked $700 million to aid lower Manhattan businesses; private partnerships have raised and distributed more. But many of the remaining 10,000 small business owners complain that hundreds of millions have yet to be distributed, a number of assistance programs favor large employers, and the bureaucracy has been difficult to navigate.

Seth Pehr, 46, a locksmith who ran a shop in the World Trade Center with two employees, received $4,100 from the city and state for several days of lost revenue and an additional $57,000 from insurance.

But he has been shut out from funds provided by civic groups, such as the New York City Partnership and the Downtown Alliance, because of rules regarding the types of businesses they support.

Far from having the $250,000 it would cost to open a new store, Pehr said, "I feel I've been cast away and dismissed as inconsequential."

Some advocates say the government failed to quickly assess the needs of small business owners. Still, faced with an unprecedented disaster, agencies such as the Federal Emergency Management Administration have taken strides to re-examine applications and revise decades-old policies.

"New York is the guinea pig for America in dealing with a terrorist attack of this magnitude," said Kathryn Wylde, president of the New York City Partnership, an advocacy group that has allocated about $9 million through grants for downtown professional service and technology businesses.

The Small Business Administration has approved about 5,000 loans totaling $410 million for businesses that have fewer than 500 employees.

The federal government also provided $500 million in direct aid for small businesses. But it took until March for the money to start flowing -- and, Wylde noted, "the average small business can exist for only three months on its working capital."

To date, government agencies have allocated only half of the money earmarked for small businesses. And shopkeepers struggling to reopen or keep their businesses afloat have grown disheartened by the multimillion-dollar grants given to 40 of downtown's largest entities.

"Large companies are frankly the engine that drives the downtown economy," said Jonathan Fair, executive vice president at New York City's Economic Development Corporation.

When plans to rebuild lower Mahattan come to fruition -- a process that could take a decade -- entrepreneurs may again find lower Manhattan a good place to set up shop. In the interim, those who remain hope to eke by.

"Being in New York has put us at a disadvantage to compete," said John Carlin, chief executive of Funny Garbage, a media and animation company in Soho that laid off half of its 70 employees. "But we're too dyed-in-the-wool New Yorkers to leave. We'll go down with the ship."