Peter Vogric is buried at the Cemetery of the Holy Rood in Westbury, just across the street from the family business he opened on School Street 35 years ago.

“He said I want to be buried there so I can keep an eye on the shop,” his daughter, Annette Farragher, said.

Fifteen years after his death, Vogric’s family worries they may no longer be able to honor his dying wish. Their business, Dependable Acme Threaded Products on School Street, is among four properties that could be uprooted as part of Gov. Andrew M. Cuomo’s proposal to expand the Long Island Rail Road’s Main Line.

“My father started this, and it took him a long time to find this place,” said Farragher, 54, of Valley Stream, president of Dependable Acme, which makes threaded rods and nuts. “I don’t know if there’s really a fight you can put up. If they want it, they’ll take it.”

The plan by Cuomo to build a third track along 9.8 miles between Floral Park and Hicksville is far less intrusive than similar past proposals, which could have required building on more than 200 private properties. However, ‎the latest version of the project, which now includes the elimination of seven grade crossings, still requires eminent domain takeovers of some businesses with deep ties to their communities.

Farragher’s mother, Madge Vogric, 85, still answers the phone in the wood-paneled offices of Dependable Acme, which her husband relocated from Brooklyn in 1982. The business has been there so long, “My car doesn’t know any other way to go,” Farragher said.

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Project officials say the business, which includes a machine shop, may have to be razed to accommodate drainage improvements and the elimination of the School Street railroad grade crossing. Farragher said her family supports getting rid of the “dangerous” grade crossing. Even if they didn’t, “we really don’t have a choice.”

The property acquisitions are part of the state’s estimated $2 billion LIRR Main Line Expansion project, set to begin this year. State and Metropolitan Transportation Authority project officials say it will ease the commutes of a half-million LIRR customers daily.

Despite assurances that the new track will be built entirely on the railroad’s existing right of way, several related improvements, including seven grade crossing eliminations, new retaining walls, drainage improvements and expanded station platforms, will require working or building on two dozen privately owned parcels.

In most cases, the property intrusions are minimal — sometimes measured in inches. Some are only temporary easements needed during the project’s construction phase.

But, under the plan, four properties could be acquired altogether, including Dependable Acme, two auto-repair shops — one on Covert Avenue in New Hyde Park and another on Urban Avenue in New Cassel — and a self-storage facility on New Hyde Park Road in New Hyde Park.

The New Hyde Park Auto Clinic and Safeguard Storage, two of the four businesses slated to be acquired, did not respond to requests for comment.

Project officials said that under Cuomo’s direction, they have gone above and beyond the state’s eminent domain guidelines, staying in particularly close communication with the affected business and property owners and guiding them through the process.

“The relocation of up to four businesses will allow us to remove crossings and dramatically improve safety, reduce traffic congestion, and reduce noise from train whistles and gate bells along the project corridor,” project spokesman Shams Tarek said in a statement. “The project team has worked hard to reduce the number of businesses that may be affected, and we’ll continue to do everything we can to make this process as easy as possible for our neighbors.”

The latest third track plan will allow critically important reliability and service improvements for railroad customers, LIRR President Patrick Nowakowski said in a statement.

The governor’s proposal “differs completely from prior proposals by minimizing the impacts of construction on local communities,” Nowakowski said. “We look forward to seeing the innovation that [builders] propose to speed construction and reduce the impacts on the communities surrounding the project area.”

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The railroad in January announced it had whittled the list of potential builders to four firms, which will all be allowed to bid on the contract to design and build the project.

Farragher said project officials have been very accommodating, but the situation remains “just a nightmare.” She worries for her four employees — two of whom live near the shop’s current location — and dreads having to move her business’ heavy machinery to a new site.

“We’re not looking at relocating as a pleasant thing,” said Farragher, who hopes project officials will allow Dependable Acme to stay at its current location by taking only part of the property. “All we’ve got to do is pray that we get to stay. That would make life a lot easier.”

According to project documents, the owners of the displaced properties will receive “just compensation” based on appraisals by the state of the properties’ fair market value. The state will also cover business’ moving and “re-establishment” expenses and other professional fees and help find them new locations “with priority given to relocation within the same hamlet or village where the displaced business is.”

The property acquisitions would begin in 2018, officials said.

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Finding a new home for their business is “not that easy” for the Hernandez family, owners of JH Auto Collision, according to the family’s Manhattan attorney, Philip Sanchez, who is negotiating with project officials for a financial settlement as part of the eminent domain takeover.

The business’ location on Urban Avenue in Westbury, next to the LIRR tracks, is ideal because it provides enough space to house specialized equipment and cars being repaired and those for sale, Sanchez said. And because the state is only required to compensate displaced businesses for the value of their used “trade fixtures,” or equipment, Sanchez said his clients could potentially take a loss if they have to replace the equipment at a new location.

“I understand why they’re doing the project, but it’s a huge disruption for our clients,” said Sanchez, who specializes in eminent domain law. “You’ve been somewhere. You’re established. People know where you are. And now you have to move, through no fault of your own.”

Assemb. Edward Ra (R-Franklin Square) said the impact to community businesses is one reason he opposes the latest third track plan, acknowledging it is less intrusive than past proposals.

However, “I think there’s always a cost to a business from having to uproot and try to re-establish somewhere when you’ve been in a community for generations,” he said.

Jerry Baldassaro, president of the Greater New Hyde Park Chamber of Commerce, said he sympathizes with the concerns expressed by local businesses, but he believes they should take full advantage of the promises made by Cuomo and the LIRR to compensate affected property owners.

“If it’s a done deal, you have to get the best deal you can, given the situation,” said Baldassaro, owner and publisher of the Town Planner Calendar of Greater Long Island, who believes most merchants’ concerns are about how long construction of the project will last.

Project officials have said they expect construction to last three to four years.