To keep it simple, I have a Spider 3 Line 6, and an Epiphone Les Paul. the only problem is it sounds like when I play it makes a weird almsot like wavy noise. I cant figure out if its the amp or the guitar

Anyone have an suggestions?
Wavy noise? I think I understand what you mean.
Is it more audible when you ring out a power chord? If so, then that's normal as long as there's no buzz.

In my world, the color RED doesn't exist.

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I know what this is. Line 6 has those presets on it. So, if the channel has a preset with echo, but you turned the knob down, it'll still have the echo on UNLESS you move the knob. So, roll the knob up, then down. I've got one of those amps, it took me a bit to figure out.
it does it like crazy on insane, and now going through power chords, it sounds like its doing it on anything G or below...
dude, how old are your strings? when my strings are really old, i get a wavy sound, almost like a vibrato. If that's the case, restringing your guitar could solve the problem.
Try another guitar and then you'll find out where is the problem!
I used to have that problem too... With me it was caused by one of the strings being a tiny bit out of tune:p Not enough to make the string flat or something but enough for weird stuff like that to happen.
Yeah, just tune your guitar. If it's in tune, you probably have intonation problems you need to get fixed.