Three days late, and $37 million into a high-stakes project to co-locate two schools, students at Benjamin Franklin High School and Science Leadership Academy are scheduled to report to class Friday morning in their new building.

Late Thursday, dozens of workers were cleaning and polishing, moving boxes, and installing features to ready the building for its occupants. They would work through the night.

But even after the round-the-clock work on the hulking building at Broad and Green Streets, the school will still be an active construction site, with sections walled off and inaccessible to students.

Some hallways Thursday were lined with boxes; others had plywood blocking off unfinished areas. The Inquirer was granted exclusive access to the building Thursday night.

In the face of staff and parent concerns that the district was putting students at risk by bringing them back with so much of the building unfinished, Danielle Floyd, the Philadelphia School District’s chief operating officer, was emphatic: “We have confidence that this building is safe for kids.”

The staffs of both schools sent Superintendent William R. Hite Jr. and other leaders a letter Wednesday expressing their concerns about students learning and adults working in the building.

Floyd said a construction manager and inspector will be on site during school hours for staff to raise concerns with, and there will be weekly meetings with staff to discuss the project. The district will be transparent about the work, she said.

“It’s still a construction project in an occupied building. We’re being very honest about that,” Floyd said.

She said she had directed the project team to be “laser-focused on cleaning. I know there were concerns about air quality, and we will be paying significant attention to that.”

Before students arrive Friday, all air filters and vents will be cleaned again.

Twenty-five cleaners were working overnight Thursday into Friday to sweep, mop, and shine the spaces that students and staff will occupy.

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Ben Franklin, a neighborhood high school, is expecting about 370 students to attend; SLA, an elite magnet, enrolls 500. SLA had occupied rented space in Center City that was costing the district $1.5 million annually, and Ben Franklin had about 1,000 empty seats.

Students will have separate entrances, classrooms, gyms, and eating spaces. Ben Franklin will occupy the Broad Street side of the building and SLA the 15th Street side.

District officials said the project, which has been in the works for two years with active construction beginning in July 2018, was hampered primarily by problems found after construction began.

“We ran into a major issue with the rebar needing to be reinforced,” said Floyd, referring to the steel bars that reinforce concrete in structures. Contractors needed to use eight to 10 times the rebar they were expecting to.

There were also problems with water entering the building, and a delay caused by the time and effort involved in relocating the school’s cafeteria from the sixth floor to the first.

“That was an expensive decision, but it was a great decision,” Floyd said of the relocated cafeteria.

Both Ben Franklin and SLA staff and students were involved in the design of the retrofitted building, which aimed to preserve the character of both schools but also give each a design upgrade.

Already evident is new air-conditioning and LED lighting, a marked improvement from the dim fluorescent lights of the old Franklin-only space. Workers were busy in the first floor cafe areas for both schools, with tables already adorned with “BFHS Strong” and the school’s lightning bolt logo for Ben Franklin, and a rocket ship for SLA.

Some classrooms were finished and an obvious improvement from the old Franklin building; others, like some lab spaces, were not yet ready. Staff have found workarounds for those classes, Floyd said.

The entire sixth floor is off-limits to students and staff, and the school kitchen is not yet ready, so students will have to eat box lunches for the time being.

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But what was clear Thursday night was the promise of the place — the natural lights, the SLA sixth-floor terrace with breathtaking views of Center City, its second-floor office space that re-creates, almost down to the furniture, the layout of the old rented space; Ben Franklin’s large patio for students to spread out, its college-access suite with high-backed, deep chairs for students to work and chat.

“It’s going to be amazing when it’s done,” Floyd said.

The project should be finished by the end of this year.