Surge protector would NOT have protected it so don't kick yourself. If you had your footswitch plugged into the amp, the surge may have ruptured components in the circuit. Most likely are components on page 2 of the schematic in the upper left corner associated with the channel selection, C77 and TR1 would be first suspects. Deeper into the circuit is the channel switch chip IC9.

A voltmeter test of the FS_B input from the footswitch to verify that with the footswitch disconnected that this approaches 5 volts is first step. If it doesn't then the three components mentioned should be tested in the order I mentioned them. If it does go to nearly 5 volts, then IC9 is likely the culprit... it is a DG212 analog switch chip. It is readily available from DigiKey.com and others... in several different type packages. If yours is surface mount, you need to find someone with the proper tools to change the chip.

Here is link to schematic: http://elektrotanya.com/marshall_mg50dfx_sch.pdf/download.html