I have seen input tune problems cause a high SWR on the output. If you put the SWR meter between the radio and amplifier, you will be able to see the amplifiers input match. Sometimes there is a variable capacitor on the input matching network inside the amp. If the amplifier has a fixed input capacitor, it can be replaced with a variable. A few pictures of the inside of the amplifier would let everyone see what you have. It is possible that something is out of place and someone might spot it. At the very least, we can figure out what the input network is.
Here is some work that i did to the input of my Texas Star 350.
Texas Star DX 350 HDV Input SWR | WorldwideDX Radio Forum