(CNN) — An emotional John Boehner spent one of his final days in office saying goodbye to friends and colleagues — and even bitter adversaries across the Capitol.

But behind the scenes, Boehner’s allies and fellow Republican leaders were moving aggressively to secure enough votes to pass one of the biggest budget deals the Ohio Republican has cut since becoming speaker nearly five years ago.

Ahead of a crucial Wednesday, when Rep. Paul Ryan is expected to be nominated to succeed Boehner as speaker, Republicans were running into a fresh set of problems as they tried to ram through the last-ditch budget deal, with lawmakers from rural states objecting to cuts to the crop insurance program and others balking at the proposal’s price tag.

In a move that helps supporters of the deal, Ryan himself backed the proposal Wednesday morning, the day after he said the process behind creating the deal “stinks.”

“What has been produced will go a long way toward relieving the uncertainty hanging over us, and that’s why I intend to support it,” Ryan said in a statement. “It’s time for us to turn the page on the last few years and get to work on a bold agenda that we can take to the American people.”

As Boehner tried to lock down votes on the House floor, a number of lawmakers refused to endorse the plan, angry that they were being jammed by their party leaders and worried about the effect the plan may have on their districts. Even close Boehner allies, like Rep. Pete Sessions of Texas, chairman of the powerful Rules Committee, suggested to CNN he was seriously weighing opposing the deal.

“Agriculture, agriculture, agriculture are my problems,” Sessions said.

The concerns spanned the gamut — including the backroom nature of the talks that produced a deal lawmakers will be forced to vote on with little time to review. Many Republicans also believe they should have won more concessions from the White House for raising the debt ceiling until 2017.

While GOP leaders still expressed confidence the bill would pass as early as Wednesday, it appeared that the final vote tally could be close and only a minority of Republicans would back a plan strongly supported by Democrats.

“I think we’ll be in a good place,” House Majority Leader Kevin McCarthy, R-California, said Tuesday night.

As House Republicans worked their members, Senate Republicans and Democrats realized they had a problem on their hands, too.

Sen. Rand Paul, R-Kentucky, planned to mount a filibuster in an attempt to delay final passage — and some rural state senators from both parties were threatening to vote against the plan. That means Senate Republicans could need roughly 20 of their members to vote to break a filibuster, a hurdle that Majority Leader Mitch McConnell will have to overcome next week.

Privately, Boehner abruptly dropped in for a brief strategy session in the office of Senate Minority Leader Harry Reid, a long-time adversary but whom he needs now to push the deal over the finish line. Boehner — who has a reputation for getting emotional — left, appearing to have tears in his eyes.

The two men — in addition to McConnell and House Minority Leader Nancy Pelosi — realized that they had their work cut out for them.

Tuesday afternoon the Congressional Budget Office informed leaders that the methods they used to pay for the deal left them roughly $5 billion short. Leadership aides from both parties downplayed the budget hole, saying the CBO didn’t give them full credit for the savings they came up with and there would likely be some technical changes to the bill, but no major revisions.

Reid said the CBO issue won’t sideline the deal.

“The number isn’t quite right, but that doesn’t matter,” Reid said. “The point is this: the CBO numbers have fluctuated for more than a week. One day up. One day down. We are satisfied with the agreement we have.”

Another problem facing leaders: Rural lawmakers sharply objected to language included in the deal that would cut into crop insurance subsidies for farmers.

House Agriculture Committee Chairman Mike Conaway, R-Texas, began circulating a letter Tuesday urging fellow Republicans to oppose the bill until the provision is removed.

“As chairman of the Ag Committee, I got to protect the integrity of the farm bill,” Conaway said. “The overall impact is to flush insurance companies out of business, which I think is the President’s intent.”

Under the deal, rate of return for crop insurance will be lowered to 8.9% — down from 14.5% — in order to cut costs and help pay for the increased spending. Republicans and Democrats agreed to raise domestic and defense spending by $80 billion over the next two years, with an additional $32 billion in emergency war funding. It would extend the national debt limit until March 2017 and make cuts to the Social Security disability program.

Conaway, along with the Senate Agriculture Chairman Pat Roberts, R-Kansas, and top committee Democrats, issued statements blasting the change to the crop insurance program, and arguing they would oppose any changes to the 2014 farm bill they negotiated.

“While congressional leaders may sell this package as providing budget stability, it is anything but stable for farmers and ranchers,” Roberts said in a statement. “Once again, our leaders are attempting to govern by backroom deals where the devil is in the details. I will continue to oppose any attempts to cut crop insurance funding or to change crop insurance program policies.”

Florida Rep. Dennis Ross, a member of the House GOP whip team, told reporters he planned to vote against the bill mainly because of the “ag issue,” but he also cited concerns about not getting more in return for suspending the debt ceiling.

On Tuesday afternoon, sources said that party leaders were engaged in a furious round of back-channel talks with the CBO to ensure that the price tag of the proposal didn’t scare away support. By Tuesday afternoon, leaders were trying to ensure that the deal wouldn’t cost more than anticipated, a potential problem for fiscal conservatives.

Many Republicans, however, were still reserving judgment — particularly since the bill was proposed shortly before midnight and could be voted on right before Boehner officially hands the speaker’s gavel over to Ryan.

Rep. Tom Rooney, R-Florida, said his district consists of seniors and farmers — two groups who are “not going to be ecstatic about some of the things that are in there.”

He added: “I’m a little frustrated that we’re doing a (whip) check right now because I have no idea.”

On both sides of the Capitol, lawmakers were frustrated about the process of being forced to capitulate on a key concession — raising the debt ceiling — without more time for debate.

Wisconsin Republican Sen. Ron Johnson called the process “disgusting” and threatened to vote against it.

Rep. John Shimkus, R-Illinois, said he was “leaning no” on the deal, pointing to the way leaders crafted the way to pay for it.
“There’s a crop insurance in there I didn’t know about,” he said.

After a Tuesday morning meeting where GOP lawmakers played a video montage feting Boehner, the Ohio Republican expressed confidence that the deal would be passed Wednesday. But Boehner, too acknowledged the process could have been a little less sloppy.

“This is not the way to run a railroad,” he told reporters, contending he had no other choice.

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