I don't think we can assume it's the head unit just because "the amp was working before". By all accounts, the "head unit was working before" too or he wouldn't be posting here stating he lost his channel. Is the amp in question also the Boom HD amplifier or are we talking about an aftermarket amp?
I guess if you're 100% certain that all your wiring is tested and perfect, I'd find a 1000Hz test tone. First thing is disconnect all your speakers. Next, turn the bike on, run the test tone on a continuous loop with volume turned to 4 clicks down from max. From there, set your multimeter to Volts Alternating Current at it's lowest setting and connect the + and - to the DMM and see what you're reading. If it's a HD Boom amp, you'd hope to see your voltage read out around 12v. Since you know which side is working, I'd start there and get your baseline. Move to the other side and see what your voltage is. Zero would be the reading I'd expect you to get. Now take the amp out of the mix and go to the output of the head unit. In this case, it's the speaker wires that would exist if the amp wasn't there or would also be found on the input side of the amp -- really just need to be upstream of the amplifier and run the same test. If you're testing the radio only output, theoretically you'll see somewhere between 8 and 10 volts from each side of the radio. I think that's really the only way you're going to be able to see if the problem is on the input side or the output side.
Those radios aren't cheap but should be readily available from a trusted seller for around $500. If need be, I can ask my crew, whom I trust implicitly, if they have an extra one laying around if thats the route you take.
If this is an aftermarket amp, the process is generally the same but I'd have a couple other questions before digging this deep in that might help. good luck