I'm not sure if your wooden-golden-wooden-golden-... setup will work.
Bettter have a continuous golden line where the wooden ones feed into.
If you have the materials for it: convert your conductive pipes to redstone conduits, so the engines will throttle themselves down (and thus use less lava), if demand is low.
Why your lava can isn't emptied in the engine? Don't know. I'll have to try it out myself now, maybe I find the cause.
edit: No clue. All four stackable lava containers (didn't try buckets) were accepted without fail, it just took a second or so for the engine to notice the containers. Worked both an redstoned and non-redstoned engines.