Joe Williams keeps a level handy in an upstairs bedroom. 

The Howard Beach homeowner is trying to measure how much his storm-damaged home is out of line nearly six years after Hurricane Sandy filled it with water. 

"The main beams that support the house are coming through the floors. So the floor joists are actually breaking through the floors," Williams said.

It's an issue Williams thought would be solved when the city's storm recovery program, Build It Back, elevated his home to protect it from future floods. 

But last year, Williams and his wife were told that their home was no longer eligible for elevation. The notice came after they had moved out so the work could begin.

"It's extremely upsetting," said Reneevee Rodriguez, a Build it Back participant.

The couple's problems began after Build it Back said it was $500 million over budget. HUD, the federal Department of Housing and Urban Development, told the city to re-evaluate every elevation project that had not begun by 2017. Build it Back then adopted a new eligibility formula that made it more difficult to qualify for help. The Williams' home did not meet the new guidelines.

"It seems like the last remaining applicants were being pushed out of the program. They weren't given the help they were supposed to be receiving," Rodriguez said.

After losing two appeals with Build it Back, Rodriguez sued, charging that the programs's financial woes were preventing her home from being elevated.

"In the beginning, there was no control over the funds. Contractors were taking advantage of the program left and right. So why is this now my fault?" she said.

A judge last month agreed that the couple was a victim of the program's poor finances, but ruled that the city's actions were not arbitrary, capricious or irrational.

The couple now face a difficult choice: appealing their case, a time-consuming and expensive process that won't guarantee their home is elevated, or accepting the limited repairs Build It Back is offering to complete.