Two knowledgeable sources say Manafort, who was recently hired by Trump to lead his delegate operation, is taking on an expanded role.
Manafort's message at the New York City meeting: There are two weeks to right the ship, figure out a real New York and California strategy and develop an outline of a conservative message.
The move raised questions about the future of Trump's embattled campaign manager, Corey Lewandowski.
Lewandowski on Monday pushed back on talk that his role is shrinking and emphasized that new hires are needed as the campaign goes forward. "This is like a small business," Lewandowski told CNN. "You start off small and there's a core group of people and then you have some success and the business grows."
"This campaign, and I've said this on the record many times, is about loyalty," he said. "Everyone on this campaign is exceptionally loyal to Mr. Trump -- and the other members of this campaign -- because we are fighting the political establishment."
Republican sources, both inside and outside the campaign, describe the GOP front-runner's operation as managed by a closed-off inner circle that rarely challenges Trump, who operates as his own top strategist. It's time to "rebuild," one top source said.
"The campaign has just entered a different phase," one source said. "I don't think anybody has to leave. But I think the circle has to expand," the source said of Trump's small team of top advisers.
Ted Cruz's recent successes and the push of the stop-Trump forces in the GOP have Trump on his heels and now needing to win 60% of the remaining delegates to win the nomination outright, according to CNN estimates. At the same time, Cruz has aggressively worked to peel away delegates at the state level and pocket commitments to back him should nobody win on the first ballot in Cleveland.
Friction between Lewandowski and Manafort may have already had an impact on Trump's campaign.
Lewandowski last week fired Trump's Colorado state director, James Baker, just ahead of this weekend's state convention, where Cruz is expected to do very well. A source confirmed to CNN that the reason for the firing, first reported by Politico, was that Baker was working too closely with Manafort. (Baker did not respond to requests for comment on the firing.)
Campaign sources say Lewandowski's role is clearly being diminished. "Manafort has really kind of taken over, and started reorganizing the campaign," a knowledgeable GOP source said.
Trump campaign spokeswoman Hope Hicks disputed the reasoning behind the firing and said Lewandowski had no role in the dismissal.
The power struggle, however, is a delicate one.
Trump is still viewed as being fiercely loyal to Lewandowski, sources say. And Trump himself has said he's not going to "ruin a man's life" over allegations that Lewandowski roughed up former Breitbart reporter Michelle Fields at a campaign event in Florida last month. Lewandowski was charged with simple battery last week and the campaign insists he will be exonerated in court.
One reason why Lewandowski is staying for now: he still receives much of the credit for Trump's rise from reality TV star to Republican front-runner.
"He's a deeply loyal guy, maybe to a fault," one GOP source said of Trump.
Manafort does not believe Lewandowski or Trump political director Mike Glassner are up to the current campaign challenges, a source, who is a longtime friend and associate of Trump as well as an ally to Manafort, told CNN.
So Manafort is urging Trump to bring in more experienced hands, while not pushing for any formal shakeup. "(Manafort) is sensitive to jamming Corey, who has a son-like relationship now with Donald Trump," the source said.
The source added, however, that Manafort would like to see a "gravitational" shift of some larger strategy roles.
Manafort consulted several veteran GOP hands late Tuesday night and Wednesday morning for input on what they think of the moment -- a rough week on the campaign trail capped by the Wisconsin loss -- and the challenges for Trump ahead. Those plans would typically be the purview of a campaign manager or top strategist, not a delegate team leader.
A veteran GOP player familiar with Manafort's effort to help Trump said Manafort believes there is a remote chance to get the 1,237 delegates needed to clinch the nomination on the first ballot -- but that the first ballot is his best shot to win.
"Manafort is an excellent floor organizer and he'll have a good team. His ability to succeed will depend on how close Trump is to 1,237 after California," this source said. "If it's 20-40 short, Manafort has a chance to get 1,237. The likelihood of success declines as that number rises."
Frustration, disconnect at the top
After the celebrity magnate railed against what he saw as unfair media coverage of his recent stumbles, one Trump source sounded puzzled. "By any measure it's the worst week of the campaign. By a lot."
The result of that disconnect, sources say, is what happened in Wisconsin Tuesday night.
While Trump thought he was going to pull off a "surprise" victory in the state's primary, all of the public polling and internal data inside his rival's campaigns were forecasting a blowout win for Ted Cruz. "I don't know who told him that," a campaign source said in frustration.
The billionaire was clearly frustrated during last week's trip to Washington where he visited with Republican National Committee officials
over the delegate rules that will be crucial at the party's convention this summer.
"Trump was disappointed that his team was not up on the delegate count," a Trump source said.
Meeting with Republican National Committee Chairman Reince Priebus, Trump and his team simply appeared unaware of how the delegate process worked, a Trump source said.
As Trump seemed taken aback in recent days by Cruz's aggressive efforts to peel away delegates in places like Louisiana, GOP strategists said such maneuvering should come as no surprise. A top Republican operative said unless Trump acts quickly, delegate raids in places like South Carolina, where the New York billionaire won handily, could come next.
Trump's adversaries see the campaign overhaul as coming too late in the process.
"Trump will not win the nomination on the first ballot, and any delegates he does get there will be his high water mark," said #NeverTrump-PAC strategist Rory Cooper. "As this becomes clearer and clearer, he's going to lash out, attempt to delegitimize the rules and get people focused on distractions."