[Arran]

I would replace the remainder of the capacitors and check the resistors for drifted values, a drifted bias resistors can cause the audio output tube/s to draw too much current making the transformer run warm. After five hours of use it isn't unusual for the top of the cabinet to get a bit warm or for the transformer to be warm as well, but not hot. If the line voltage is a bit high that can also cause the transformer to get a little warm if it's a 60 cycle unit, the 25 cycle ones don't seem to be bothered as much since the core is larger and takes longer to saturate.
Regards
Arran