BEFORE their full-scale battle with President Clinton over the final shape of the fiscal 1996 federal budget, majority Republicans on Capitol Hill must first thrash out their own differences on funding the armed forces. At stake in the intra-GOP fray are the fates of some of history's most costly and sophisticated weapons systems, and the fortunes of dozens of defense contractors and thousands of jobs in an industrial sector already reeling from massive post-cold-war cutbacks. The outcome could also affect the political prospects of legislators across the nation if they fail to preserve defense programs that bring work and money to their districts. ''It's going to be a wild conference,'' a GOP congressional staffer says of the deliberations now under way to square divergent versions of the fiscal 1996 defense budget produced by the House and Senate last week. House-Senate conferees are likely to resolve many of the mismatches as they work on compromise legislation. But heated debate and tough horse-trading are expected over several big-ticket items, including proposals to build a third Seawolf submarine and expand the fleet of B-2 bombers. While the House GOP won new B-2 funds, their more fiscally cautious Senate compatriots sided with the White House in deciding not to exceed the 20 Stealth bombers already authorized. The Senate also heeded Mr. Clinton's call for a third Seawolf; but the House rejected the $1.5 billion project. There should be no haggling on the size of the defense budget, though. Most Republicans and some Democrats in the House and Senate accuse Clinton of excessive cuts in military spending. The Senate passed a defense budget of $265 billion for the year beginning Oct. 1 - $7 billion more than was sought by the Clinton administration. House Republicans approved $267 billion, but have agreed to pare down to the Senate figure. The conference committee's goal is to reconcile ideas on how the money should be spent. ''Obviously, the two big contentious items are the Seawolf and the B-2,'' says Baker Spring, a defense analyst at the Heritage Foundation, a conservative think tank in Washington. ''If I had to choose in terms of meeting funding requirements, the B-2 would probably be my preference.'' The House agrees. Last Thursday, it voted 213 to 210 to defeat an amendment that would have eliminated $493 million to begin building two more of the bat-winged Stealth bombers. Supporters see the pair as the first of 20 additional B-2s that they contend are crucial to US national security. But the administration and the Joint Chiefs of Staff won Senate opposition to more B-2s, in part by arguing that funds would be better spent on precision munitions like laser-guided bombs. Eager to keep their promises to balance the federal budget and cut taxes, Senate Republicans were also put off by the huge cost of the B-2. Northrop Grumman Corporation says it can build 20 more for $13 billion over 13 years. Critics assert that operating the planes would push up the final price tag to more than $30 billion. Many analysts say that B-2 supporters will have a hard time saving what opponents call a ''turkey'' because of the plane's cost and lingering doubts over its radar-evading ability. These analysts cite opposition to the B-2 by some of the most powerful Senate leaders and the slim margin of last week's House vote. In addition, influential House Budget Committee Chairman John Kasich (R) of Ohio plans to take his campaign to kill the program to the conference committee. ''There will be plenty of people in conference who will oppose the B-2,'' predicts Mr. Kasich's spokesman, Bruce Cuthbertson. FEW analysts, however, were willing to speculate about the fate of the Seawolf. The administration says the third vessel of its type is required to preserve US naval superiority and to keep its maker, Electric Boat Company of Groton, Conn., in business long enough to begin production of a new generation of nuclear-powered attack submarines. The Senate agreed. The House, however, voted to cancel the program, saying it was too costly a way of keeping Electric Boat afloat. Instead, it approved about $1 billion for Electric Boat to upgrade the second Seawolf, now under construction, and continue work on the new attack submarine. The House earmarked another $150 million for Virginia-based Newport News Shipbuilding Company to develop new submarine technology. An important factor in determining the fate of the third Seawolf could be the amount of support Electric Boat and Newport News command among conference committee members.