Yeah, be nice if the loop allowed boost as well as cut. You would have thought it would be simples but hey, I don't design firmware for a living so what do I know.
On the sucky thing. Fair enough, if you hear it - you hear it. Might be worth checking.
1) Inputs: I run mine as input 1 = guitar, input 2 = Variax. If you don't, it might be worth trying.
2) Input Impedance (system setting, set per-patch). I tend to leave mine at the default but it can have an effect on the tone so it might be worth playing with. Higher impedance settings tend to give a harder, brighter, more focused tone and it is a taste/guitar thing.
3) Input Pad switch. I tend to run mine with the Pad switched on so that, if I plug in a weedy single coil guitar, I can turn the pad off and bring the gain levels closer to the meatier humbuckers. I think it just cuts gain but it may be worth fiddling with.
Some people have gone so far as to include a line box between the POD FX Send and Amp input to try and sort out any impedance mismatches but I don't know if that would help you.
Luck.
JIM