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Judge Doyle Square - Exact Sciences building

This rendering shows JDS Development's proposal for Judge Doyle Square, which features a corporate headquarters for biotech Exact Sciences Corp.

Madison’s finance committee is scrutinizing pieces of a complex, emerging deal with JDS Development on the massive Judge Doyle Square project south of Capitol Square.

During an update from city negotiators Monday, the Board of Estimates raised a series of questions about financing and parking for the $202 million redevelopment that would bring a new headquarters for booming Exact Sciences Corp. and a hotel for Monona Terrace to blocks that hold the Madison Municipal Building and Government East parking garage.

Board members questioned the completeness of JDS’ recently submitted tax increment financing (TIF) application, the developer’s submissions on equity and debt, the loss of Government East parking during construction, and the design and uses of parking.

City project manager George Austin and planning, community and economic development director Natalie Erdman said progress is being made in many areas and that negotiations continue on unresolved issues.

Mayor Paul Soglin said the project challenges the city’s commitments to compact urban development and public transit versus sprawl. “If a project like this can’t work, basically we ought to throw in the towel,” he said.

Soglin and JDS signed a development agreement on July 14 and the sides are negotiating unresolved issues. Under a deadline set by Exact Sciences, they must bring an amended agreement to the Board of Estimates on Aug. 24 and City Council on Sept. 1.

Under the agreement, JDS would bring $44.3 million in equity and $89.3 million in borrowing for a total of $133.6 million in private investment, the TIF application says.

The city would invest $42.5 million in TIF for private elements of the project, including $12 million guaranteed by jobs to Exact Sciences to help build its office building, a $9.7 million grant to help cover costs of property, and $20.8 million to build 650 private parking spaces, which would be owned by the city and leased to JDS.

The city would use $18 million in parking reserves to build 600 spaces to replace Government East as well as $1.3 million for 40 spaces for city vehicles and $1 million for a bike center.

City negotiators are compiling a list of incomplete information on the TIF application and are in the process of verifying JDS commitment letters on equity and debt, Austin said Monday.

Replacing parking during construction is a challenge, Erdman said.

The city is exploring access to hourly parking in a new Anchor Bank garage to be opened in late 2016, studying the impact of relocating Municipal Building staff during renovations to that building in 2016, identifying shuttle opportunities and more.

“We have a long way to go,” Erdman said.

Ald. David Ahrens, 15th District, questioned the current plan to dedicate just 50 spaces to a hotel that will have 216 to 250 rooms. Ald. Maurice Cheeks, 10th District, wondered if limited parking for the hotel might undermine efforts to secure a national operator.

Austin and Erdman said the hope is to deliver hotel parking through smart management of the 1,250 spaces. A redesigned garage would put public parking above ground and one grade below ground, and private parking below ground, Austin said.

In a two-page letter to the city on Monday, a group of major Downtown landowners welcomed the project but also voiced concerns about parking.

Concerns include subsidizing parking so it’s essentially free to the developer, a failure to maintain Government East’s parking during construction, and a design that doesn’t maximize potential stalls and chews up available above-ground space.

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Dean Mosiman covers Madison city government for the Wisconsin State Journal.