I want to get a really clean signal for my guitar but the amp I use to record with (Using the FX loop) only has two gain stages (VX Kraken has gain 1 and gain 2 but no clean). I've tried plugging my guitar into the interface but the signal is so quiet that it just doesn't work. There's nothing wrong with the guitar (I've checked). Any suggestions?
This is normal: guitar out is pretty low as it is expected that you will gain the heck out of it. You can adjust the level in the recording device/software track mixer but try for +0dB rather than boosting till you hear it. If this is a software DAW, then just add a VST gain stage to the track to help you hear it better. VST effects are usually applied in realtime after the recording stage (they need a track to work on), so your clean signal will still be clean on the recording.
The track will still be clean. Instead of a adding a VST on the track, you could also set it up so that the output is to a "reamp box"--kind of like a DI but for the reverse purpose (don't use a DI in reverse, it isn't the same thing AFAIK). From the reamp box, you can go to the amp's HiZ guitar-in.