A 5 speed gearbox will give you over drive with a ratio of 0.865. I did a 5 speed conversion in my KE20 (Here) way back when. I like the KE70 box length, even though you have to cut a bit of tunnel away to fit the shifter in. The shifter position is just right (for me anyway). I think the KE55 boxes are slightly shorter, but by how much I don't know.
The gearbox conversion should make highway driving a little more bearable. I would try and avoid going for a lower ratio diff because the 3K doesnt have the torque to cope with it. Do the gearbox first, then see how you go.
Gearboxes in the FAQ: http://www.rollaclub.com/faq/index.php?title=Manual_Gearbox