Clearer documentation for some of the basic concepts, like coins, magic if you keep it, etc would be nice. A way to copy research without bird feathers would be great as well.
Updating the mod to the latest version of DF should be fairly important - it would be better to add stuff after the update than to add stuff only to have to update it 2 weeks later.
If you really want to decrease the b-w and b-e menus, you could have one building for each general profession (1 stoneworker, woodworker, smelter, forge, etc) which is upgradeable with increasing costs for each tier upgrade. The upgraded workshop would have all of the reactions of the previous tier, plus some new ones. For example, tier 1 forge would be like the current finishing forge - only coldhammering the weak metals like copper and bronze. It could be upgraded to tier 2, with some iron/cobalt and coke maybe, with the reactions of the finishing forge as well as basic weapons/etc made of metal. It would continue gaining tiers and reactions, with tier 3 requiring steel for greatweapons/armor, all the way up to the golemforge reactions at tier 7 or 8. Some of the more advanced upgrades could have probability similar to the current researching system, or all of the upgrades could require initially easy and increasingly hard research. Hopefully by tier 2-3 you will have a manger, and won't have to search through the looooong list of reactions for the one you need