1) Did the amp work before you overhauled it? If not, the problem could be unrelated.
2) I'd stick with the 5Y3 in that amp. It has a higher voltage drop.
3) What do you mean, "475 v on the top and near 515v on the bottom"? One side of the filter caps should be grounded.
4) What are the voltages on the output tube pins? Are you missing screen voltage maybe? Higher than normal voltage shouldn't cause those symptoms and could be in part because the tube is barely conducting.