President Reagan yesterday signed the catch-all spending bill needed to fund much of the federal government through next September, but he emphasized his unhappiness with Congress for not funding two key defense items fully, the MX and Pershing missiles.

Reagan's last-minute approval of the continuing resolution for eight Cabinet departments and assorted federal agencies for the rest of the 1983 fiscal year ended a budgetary confrontation between him and Congress.

The president threatened to shut down a large part of the government and furlough about 350,000 employes in an effort to force the lawmakers to reflect his priorities in the spending bill and other legislation considered during the lame-duck session.

While Reagan's veto threat deterred Congress from funding a jobs-creating bill that he opposed, the president said he is not altogether pleased with the bill he signed.

"Unfortunately, this resolution also contains a number of provisions about which I have serious reservations," the president said in his statement.

"For example, the bill fails to provide specific funds for production of the Peacekeeper [MX] missile. While I am disappointed in the congressional action on this vital strategic forces program, the language of the conference report does enable us to keep to our schedule for initial deployment in 1986 once the Congress approves a permanent basing decision . . . .

"A similar problem is the failure of the resolution to provide full production funding for the Pershing II missile," the president added. "We are developing this missile along with the ground-launched cruise missile in order to meet an Allied request for land-based systems in Europe that would help maintain deterrence."

Reagan then complained about Congress' decision to cut foreign aid spending by $571 million while increasing economic aid to Israel.

He also said that continued funding of current grants under the Legal Services Corp. until the Senate has confirmed a new board may violate his constitutional right to make the appointments. Reagan said he has asked the attorney general to review the action.

"After taking all factors into account," the president concluded in his statement, "I think that this effort has been worthwhile. Together, the administration and the Congress have agreed on a continuing resolution that will complete the 1983 budget process with reasonable funding. I thus take pleasure in signing H.J. Resolution 631 and ask all federal employes to provide the most effective and efficient services available for the taxpayers' hard-earned money."

Reagan praised the session for two major reasons.

He said the bill he signed marked the first time since 1980 that Congress has "completed action on a budget for the full fiscal year before final adjournment." And he said the level of funding in the resolution is "consistent with the budget resolution adopted earlier this year by the Congress."

"On balance the resolution is a significant achievement in our efforts to control discretionary spending," the president said. "We must keep a tight leash on federal spending. The Congress has taken an important step in the right direction."

He praised the restoration of educational and other benefits for veterans' children, saying that spending for that program was "mistakenly reduced" in the 1981 budget.

But aside from claiming those victories, Reagan lost on most of the items on his legislative agenda.

These include passage of regular appropriations bills rather than the emergency continuing resolution, plus several major administration initiatives: the Balanced Budget Amendment, regulatory reform, enterprise zones, the Clean Air Act, immigration reform and alteration of bankruptcy laws.

The 5-cent-a-gallon gas tax increase Reagan proposed was still under consideration on the Hill last night.

Still, the president's aides were claiming that the session was a victory for Reagan.

"We got everything we hoped for except for the MX and Pershing," said one Reagan aide after the president held a morning meeting with White House chief of staff James A. Baker III, deputy chief of staff Michael K. Deaver and White House counselor Edwin Meese III to go over the continuing resolution and make a final decision on whether to sign it.

According to one source, they concluded that, while they had neither won nor lost on the missiles issue, by signing the resolution they were buying additional time to argue that the missiles are necessary for national security.

Presidential aides also argue that he is doing well in building up the nation's military defenses and reducing government spending, administration priorities since the 1980 campaign.

"A lot of the items we lost on were not so much victims of the opposition but victims of the clock," said White House spokesman Larry Speakes. "Time ran out on them.

"So we probably laid groundwork in the lame-duck session for these things to move rapidly thorough the new Congress. All in all the 97th Congress was a good one for the president. We of course would like to get everything we ask for, but no president ever gets that."

David R. Gergen, White House communications director, said the administration's accomplishments in the lame-duck session are better than they appear.

"Our very strong view," he said, "is that the substance of the lame duck has been much better and more positive than the perception."

Gergen added that the administration is determined to end arguments over the fiscal 1983 budget this year so that in January it can begin pressing "a whole new agenda."