The transition period in his new government-by-shakeup may be "orderly," as President Carter promised yesterday, but one thing is plain -it will be months before the vast federal establishment recovers.

Departments hit directly by the top-level changes will be run by lame ducks, learners and retreads, which could have crucial bearing on key policy and panning decisions for the remainder of Carter's term.

Overlooking for a moment the obvious psychological impact on subcabinet officials of the sudden changes, fallout will shower Congress as well.

The power brokers on Capitol Hill have become fully comfortable only in recent months with the names, faces and thoughts of the Carter appointees. They now must revise their scorecards.

As they are doing that, the presidential nominations for the top jobs - at least three of which went to the Senate yesterday, with more to come -- must go through the sometimes time-consuming confirmation process.

As the dust Tempestuous Thursday and Fated Friday settled, the feeling in most executive branch agencies yesterday was that the big changes have been made, for now at least, and business can proceed as before.

But interesting questions arise as Carter's new Cabinet and subcabinet appointees, whomever they may be, move into their offices.

Who, for example, will decide what to do with the mass transit programs at the Department of Transportation?

DOT will have a 30-day caretaker secretary, W. Graham Claytor, a former railroad executive who will move over from the Defense Department.

He -- or the nominee who follows him -- will have to find a successor to Gary Gayton, who climbed on board the outgoing express bus with Secretary Brock Adams yesterday.

Gayton was acting administrator and deputy administrator of the Urban Mass Transportation Administration. His departure leaves no one in the top two jobs at UMTA.

If there was uncertainty about other departures at DOT, Joan Claybrook, the often outspoken and militant head of the National Highway Transporation Safety Board, indicated that she thought she would be staying.

Another question: what about the extension of the Higher Education Act that Rep. William D. Ford (D-Mich.) has been shepherding tenderly through his House subcommittee?

After months of negotiations with Joseph A. Califano Jr., the axed secretary of health, education and welfare, and his subalterns in education, Ford was nearing the final touches on an extension of the higher education law, which expires next year.

"The secretary is gone. The commissioner of education is gone. The undersecretary of HEW is gone. The head of the National Institute of Education is gone. Who do you talk to now that is a policymaker?" Ford wondered.

The undersecretary, Hale Champion, whose previously scheduled departure became an accomplished fact yesterday when he delivered his office keys to his secretary, touched on Bill Ford's concerns. His successor was to have been Barbara Newell, president of Wellesley College. Her status is now uncertain.

"Many people at HEW) are unhappy," Champion said, "but they are equally concerned about continuity of programs."

Continuity. Who now, as Patrica Roberts Harris moves over to Califano's desk from her post at housing and urban development, will speak and deal for the administration on such other burning issues in Congress as hospital cost containment and welfare reform?

Califano and Champion have been the administration's point men on both issues.

The rumor mill at HEW, for what it's worth, produced another unconfirmed tidbit yesterday -- that Dick Warden, Califano's assistant secretary for legislation, also might be leaving.

Harris yesterday asked all top staff at HEW to remain in their jobs at least until Sept. 30 to provide an orderly transition.

Said a high-level source: "Ultimately, you can expect to see the people immediately around Califano go -- Ben Heineman Jr., Fred Bohen and Dick Warden." Heineman is an assistant secretary for planning; Bohen an executive assistant.

With the White House having set noon yesterday as the deadline for Cabinet secretaties and agency heads to return Hamilton Jordan's "report cards" on high-level aides, the feeling in most agencies was that lesser heads will be rolling, perhaps as early as next week.

At the Department of Justice, there were no purge expectations -- Griffin B. Bell, after all, was not fired and his successor, Benjamin R. Civiletti, long has been groomed for the job.

Bell, albeit a trifle tardy, fired off report cards on 70 subordinates, saying he recommended no changes and ddn't expect any to be made, Justice, however, will have to fill a couple of previously vacated top jobs.

Evaluation forms were being filled out at the Department of Agriculture, where the feeling persisted that Secretary Bob Bergland and his deputy secretary, Jim Williams, remained "safe."

Bergland kept smiling. He walked into a meeting yesterday morning, cup of coffee in hand, and said tersely, "This is not Kool Aid."

Across the Ellipse from Agriculture at the Department of Interior, there was no inkling at high levels that major changes would occur on the team of Secretary Cecil D. Andrus.

Andrus, it was noted, has been the kind of Team player" the White House seems to be intent on keeping around. A skilled politician in his own right, Andrus made certain from the start that his lines to Jordan remained open, and he included political types -- Georgians among them -- in his top appointments.

At other environmental outposts -- the Council on Environmental Quality and the Environmental Protection Agency -- there was curiousity, but no evidence yesterday that heads would roll.

Said one EPA source of Douglas Costle, the administrator whose work has drawn barbs from environmentalists: "Doug's safe. When has he ever been disloyal?"

Energy, of course, with James R. Schlesinger leaving the secretariat, will have new faces His under-secretary, John F. O'leary, resigned weeks ago and another assistant, Dale Myers, recently departed.

Continuity, Doe's most vehement critics on Capitol Hill have maintained all long, is another kind of problem. This national malaise, with its roots in energy, they like to say, is a result in part of Doe's continuity - consistently wrong decisions, wrong data and wrong faces. CAPTION: Picture 1, Schlesinger opens way for "one who is less scarred." By James M. Thresher - The Washington Post; Picture 2, Claytor: Acting transportation secretary now, deputy defense secretary later. By James K. W. Atherton -- The Washington Post