You can only have one custom colour set for Juni with original KS*. KS+ and KSEx both support entirely custom characters which can be changed during the level. Even better, both mods use the same sprite sheets**, so your choice of mod isn't restricted by choice of custom character. There's a collection of
existing custom characters here.
There aren't restrictions to the size of music/ambiance files you use. However, when the track loads the game stutters. I'm not sure if there's a connection between the length of the pause and the length of the track. On fast machines it's barely noticeable anyway.
*The software KS is made with was designed so these kind of graphics are embedded. It's quite difficult to load external graphics onto moving objects. Even changing the colour of a graphic is tricky because you have to tell it exactly which colour it's replacing. Allowing the level designer to declare what colour to replace could result in glitchy behavior.
**You have to convert them for KSEx, but there's a tool for that.