Congressional negotiators, settling most of their differences over a $600 billion catchall spending bill, agreed yesterday to sell Stinger antiaircraft missiles to Bahrain, continue foreign aid to Pakistan and delay sanctions against cities that do not meet air pollution standards.

In another breakthrough that moves Congress toward the end of its session, House and Senate negotiators reached an agreement on a bill raising $9 billion in taxes in 1988 and $14 billion in 1989. The package, which would increase levies mostly on corporations and wealthy individuals, was worked out between the chairmen of the congressional tax-writing committees in a nonstop 6 1/2 hour meeting. It later was informally approved by other members of the House and Senate conference committee.

Despite progress on taxes, several major areas of disagreement blocked final conference committee action on the omnibus appropriations measure that is one of two bills needed to complete the Nov. 20 budget accord between Congress and the White House calling for a reduction of the federal deficit this year of at least $30.2 billion.

The continuing disputes, which will be taken up when the conferees resume negotiations today, include the issue of sending new humanitarian aid to the Nicaraguan contras and whether to include in the massive spending bill a provision enacting the "fairness doctrine."

Depending on the outcome, both those issues could provoke a veto by President Reagan, who has said he will not sign the appropriations measure if it eliminates non-lethal aid to the Nicaraguan rebels and if it incorporates the fairness doctrine, which would require broadcasters to air opposing sides of controversial public issues.

The chances of a continued stalemate over aid to the contras grew yesterday as House Democrats voted overwhelmingly in a morning caucus to oppose the Senate's position on contra aid. Unlike the House, which included no further aid in its version of the spending bill, the Senate voted to send another $9 million, plus as much as $7 million more to transport the humanitarian assistance that would be limited to food, clothing, shelter and medical supplies.

Several key Democratic lawmakers predicted that as many as 100 of their party colleagues would oppose the spending bill if it includes any further aid to the contras. Many Democrats are particularly opposed to what they regard as a loophole in the Senate version that would permit the new transportation assistance to be used to deliver previously authorized military assistance.

"Clearly a vast majority {of the Democratic caucus} wants no contra aid," said Rep. David E. Bonior (D-Mich.), the Democrats' chief deputy whip. But Bonior and other leaders predicted that many Democrats would eventually accept a compromise pushed by the House leadership that would provide about $5 million to the contras through the end of February and close the military aid loophole.

Nonetheless, a lingering stalemate on contra aid that could delay congressional plans to adjourn for the year this weekend is still possible if the Senate and the Reagan administration stand fast behind the Senate's version. Republican congressional leaders were seeking a meeting today with Reagan to discuss continuing disagreements on the deficit package, including the contra aid issue.

State Department officials involved in the contra policy said yesterday that they believe the White House is going to push for the House to accept the Senate version unchanged. In particular, these officials said, the administration will not back down on language that would permit already stockpiled lethal aid to continue to be flown to contra troops along with non-lethal shipments.

The omnibus appropriations bill, which would fund most government operations through the end of this fiscal year on Sept. 30, would reduce the federal deficit by $7.6 billion this year. The cuts include $5 billion from defense, which would leave Pentagon spending authority at $292 billion, and the remainder in discretionary domestic programs such as education. The other measure needed to complete the Nov. 20 budget accord between the administration and Congress would cut the deficit by about $26 billion more, through a $9 billion tax increase, cuts in permanent government programs such as Medicare and farm subsidies, asset sales and user fees.

The conference committee on the huge spending bill settled numerous disagreements yesterday. The commitee voted to:Permit the sales of between 60 and 70 shoulder-fired Stinger antiaircraft missiles to the Persian Gulf sheikhdom of Bahrain. Any unused missiles would have to be returned after 18 months, or sooner if an alternative air defense system is available. {Details, Page A25.}

Allow the administration to continue sending economic and military assistance to Pakistan if the White House grants a waiver to current law barring aid to countries that have nuclear weapons capabilities but which do not submit to international inspections. The bill clears the way for $480 million in aid this year. {Details, Page A10.}

Delay by eight months until Aug. 31 the imposition of federal financial penalties against about 60 metropolitan areas that do not meet U.S. clean air standards for carbon monoxide and ozone by the end of this year.

Appropriate $700 million for research and development of the Midgetman missile, a mobile, single-warhead weapon.

Abolish the State Department Office of Public Diplomacy for Latin America and the Caribbean, which played a leading role in promoting the administration's contra aid program.

Give most federal employes a 2 percent pay raise this year, except for members of Congress, judges and senior executives, who will get no increase.

Bar Japanese construction firms from participating in some federally funded public works projects unless U.S. companies are allowed to compete freely for construction projects in Japan. Supporters of the prohibition, which is aimed at Japan but does not specifically name it, are seeking to extend the ban to all federally funded projects.

Strip from the bill a House provision that would have expanded the alien amnesty program by barring the deportation of spouses or children of aliens granted citizenship under the 1986 immigration act.

As negotiators on the appropriations bill worked to resolve remaining differences, key conferees on the second measure met privately to settle their disagreements over the bill's tax and Medicare provisions.

The compromise on the tax bill came only after House Ways and Means Committee Chairman Dan Rostenkowski (D-Ill.) and Senate Finance Committee Chairman Lloyd Bentsen (D-Tex.) abandoned the exchange of offers and counteroffers they had been pursuing for the last three days.

During their marathon session, they agreed to limit a method by which defense and construction contractors defer payment of taxes, but not to terminate the method, as the House originally proposed. They also agreed to speed up estimated-tax payments by corporations, but in an unusual bargain decided not to count all the revenue it raised. The package thus would increase revenue by $9.8 billion next year, but only $9 billion would be counted for deficit-reduction purposes.

Even before last night's agreement, the two sides had settled on the tax provisions that would most affect individuals. The compromise would maintain the current 3 percent tax on telephone service, limit interest deductions on home-equity loans to loan amounts of $100,000 or less, freeze the top rate on estate and gift taxes at the current 55 percent for five years, require employers to pay Social Security taxes on tips earned by their service workers and crack down on large "family farms" that use an accounting technique to postpone paying taxes. It also would delay stiffer penalties on individual taxpayers who pay taxes on an estimated basis, until next year.

Rostenkowski and Bentsen also agreed to limit the deduction for interest on a home mortgage to a total of $1 million for up to two residences. And interest on additional debt, such as a home-equity loan or second mortgage, could only be deducted for amounts of $100,000 or less above the outstanding debt on the home.

Staff writer Joe Pichirallo contributed to this report.