"I am currently trying, however, to get jackolanterns and pumpkins to become fuel. When I insert these into a furnace manually, they act as i'd expect, burning for as long as I expect them to.

However. When these new FUEL items are placed into a hopper that feeds into the FUEL slot of the furnace, they refuse to go in."

This is not currently possible in a good way with the Bukkit API. Future APIs will hopefully work better, but I won't be fixing this for the Bukkit version.