Major blunder today.

I was swapping out speakers on my epiphone valve junior and after disconnecting the speaker I didn't realize that the amp was still on. After 10 minutes, I discovered my mistake. A mic with a cm element was plugged in. I immediately turned it off. I reconnected the speaker and turned it on to test the amp. I plugged in a guitar. When the volume knob was past 2 o'clock, the sound was intermittent, in and out like waves. When there was nothing plugged in and I turned the volume knob past 2 o' clock, I heard intermittent white noise. I assume that this is not normal. I believe (although I am not sure) that intermittent (on/off) sound is probably realted to the output transformer. Is this correct or what did I just damage?
And if it is the output transformer, can anyone recommend a comprable replacement that costs less than $100. I heard people have used heyboer or hammond. is the following a direct replacement for the version 3 output transformer:
http://www.hammondmfg.com/jpeg/125CSE_B.jpg .Also, would it be a good time for a slight upgrade, such as this
http://www.hammondmfg.com/jpeg/125DSE_B.jpg .For instance, a transformer that allows for a 6V6 or would that change the character of the amp?. I don't want to use Mercury as they are too expensive (beyond the cost of a new epi!).