After months of wrangling, the National Defense Authorization Act conference report is done and in the hands of lawmakers, and is expected to get a vote on the House floor as soon as Thursday.

But most conference committee Democrats did not back the compromise over an ongoing dispute about how Republicans elected to meet President Obama’s military budget requests through discretionary funding, instead of tackling the sequestration caps that are hamstringing spending across the government. Obama has already threatened to veto the legislation over such concerns.

“I agree…this is an appropriations issue,” House Armed Services Committee Ranking Member Adam Smith (D-Wash.), who did not sign the conference report, said at a news conference announcing the report on Tuesday. “The two are actually very closely linked, and it is that linkage that has me opposing this bill.”

The compromise measure includes an authorization for sending lethal defensive aid to Ukraine and supplying direct arms to Kurds and other Sunni Arab groups if the Iraqi government is deemed not to be inclusive enough; it lays the groundwork for replacing Russian rocket engines with domestic ones; and includes language that slightly stiffens the procedure for transferring Guantanamo detainees to third countries, while banning outright transfers to Libya, Syria, Somalia and Yemen — as well as those within the United States. The conference report also urges Obama to send Congress a plan for the base’s future — or closure.

Senate Armed Services Committee chairman John McCain (R-Ariz.) stressed that the conference report would have gone further on Guantanamo if the White House had offered up a plan.

“If the administration complains…then it’s their fault,” McCain said. “They never came forward with a plan that we could have probably supported in order to dispose of this issue.”

The measure also includes a full ban on torture for all agencies, something that McCain stressed would ensure the country “will never again be able to do things that they did before, which were such a terrible stain on our national honor.”

The compromise includes cost-saving measures as well, such as a one-year increase in co-pays for non-active duty personnel purchasing prescriptions drugs through regular pharmacies under the military’s TriCARE health-care program; a more egalitarian approach to military acquisition that puts more power and responsibility in the hands of service chiefs; and provides some cost savings from the reduced price of fuel.

Committee leaders congratulated themselves on the changes, and that they met the White House’s mark, authorizing “exactly the amount of money the president requested for national defense,” House Armed Services Committee chairman Mac Thornberry (R-Tex.) said. In total, the conference report authorizes $611.9 billion for various programs.

But about 15 percent of that funding comes through discretionary money designated for Overseas Contingency Operations – a workaround for sequestration caps that Democrats find objectionable. All but one of the House Democrats on the conference committee, and all but two of the Senate Democrats, refused to sign the report solely over the OCO funding provision, according to staff. Sens. Tim Kaine (D-Va.) and Joe Donnelly (D-Ind.) did sign the report, staffers said.

Democrats were also quick to point out that while the changes freed up some funds to reinvest in other military priorities – such as retirement funding — it didn’t secure enough money to expand the Department of Defense’s activities as planned for in the long term.

“There is some excellent reform there,” Smith said. “But there is, at least in the first 10 years, not savings.”

Smith also argued that Congress had to lift the budget caps through more than just a year of slush-fund budgeting “so the Pentagon can begin to make rational plans.”

Meanwhile Senate Armed Services Committee Ranking Member Jack Reed (D-R.I.), who also opposes the measure, said he feared that not addressing sequestration now would “give some people an excuse not to do it” at all.

In all, the conference committee leaders said they had to wrestle through 874 differences between the House and Senate NDAA bills. Of those, a motley crew of issues – including closing Guantanamo, proposed changes to military compensation and retirement, and lingering concerns over whether preservation requirements for that strangest of birds, the sage grouse, would hamstring certain domestic operations – had gummed up the works over the last several weeks.

But Republican leaders from both chambers emerged from the conference process lauding the merits of what Thornberry called a “good bill.”

“We reached an agreement, and it’s not everything that I wanted or what the House wanted, but I think it’s a very important reform bill,” said McCain.