I've used the sonic bass feature a bunch of times since I picked up my sp404
And I've noticed sometimes esp with certain frequencies, something that sounds on key to me will later sound off key
Does anyone know of some kinda software or website that will check the exact key of sounds so I can b 100 percent sure? It'd be super helpful

It might be worth using the subsonic effect whilst using headphones. The vibrations from your speakers could be resonating random objects to make it sound in tune at that point.

There isn't software that does that, but I have heard the new Ableton 9 has some crazy harmonic thing that can analyze notes used.

I sometimes use a guitar tuner on my phone, but this can be inaccurate too.

I don't use subsonic alot, but I use a guitar tuner for tuning my monotron. Slightly off tune sounds pretty cool to me.

if you use your 404 full blast you need the turn the bass down lots after you resample the note this will help tune it, if you can tune the root bass note, it will usually pitch nice in a nother sampler.