Specifically, per the Reorganizing Government Act of 2025 (identical bills in the House and Senate to amend and resurrect a presently expired U.S. code chapter), 90 days means "90 calendar days of continuous session of Congress after the date on which the plan is transmitted to Congress."
The import of that is: any Trump 2 presidential reorganization plan would be subject to a very specific, and not all that lengthy, ticking clock.
Created by Douglas Lucas in mid-May 2025 as a footnote for his June 4, 2025 article at Rolling Stone titled Republican bill would legalize DOGE and let Trump dismantle everything: The Reorganizing Government Act is a longshot in the Senate, but that could change--and so would the separation of powers. MSN and Yahoo republished the article without paywalls. See also the accompanying blog post with extra material.