... I just used the octagon manifold from my old round 5gal tun which only occupies half of the bottom of the tun. Would making a square manifold the occupies the entire bottom solve this?
If you are fly sparging, I would definitely recommend a new manifold. If you are batch sparging it's a little less important, but if you are having recovery problems, it's probably worth the $ to have a manifold that matches your system. If your manifold is costing you wort w/every batch, it'll pay for itself quickly enough.