House and Senate conferees put the finishing touches on the rice, cotton, sugar and honey portions of a farm bill yesterday but remained in a stubborn standoff on other vital parts of the legislation.

As the negotiators worked under pressure to send a final version to the House and Senate floors by early next week, they remained at odds over food stamps, dairy and grain price supports and income subsidy sections.

One of the other roadblocks, a dispute that had gone on for days over cargo preference language, was settled with a compromise on the terms for shipping government-sponsored grain exports in U.S.-flag vessels.

Shipping interests, represented by Merchant Marine and Fisheries Committee members, had resisted broadening the exemptions for cargo preference, which farm state legislators had sought to stimulate exports.

The compromise was similar to Senate-adopted language that would allow, under certain conditions, more than 50 percent of government-generated cargoes to move on U.S. ships.

Conference action yesterday included:

*Lower price supports for honey, in a step aimed at cutting government costs, instead of the Senate plan to phase out the support program.

*Abandonment of Senate-sponsored programs to give soybean growers a $1-per-bushel subsidy on the 1985 crop in return for lower price supports, and scuttling of a similar one-time-only payment to sunflower growers.

*Approval of a freeze of sugar price supports at current levels, with a requirement that the administration adjust import quotas to eliminate the possibility of federal spending on the domestic support program. In a move aimed at Cuba, the conferees barred the entry of quota sugar transshipped from nonquota countries.

*New programs for cotton and rice that would meet the administration's demand for lower price-support levels, yet maintain only slightly reduced income subsidies.