Simple, passive way to remove high frequency interference from low power audio
Can you show us a picture of exactly what you removed? (and maybe the input circuitry)
Any filtering will likely take place after the input amplifier, so it's possible something else is happening.   

It certainly wouldn't hurt to add a simple RC filter just in case though, then if the problem persists you know it's something else.
If you do this I would go for something like Olin suggests but adjust the values for your guitar pickups (e.g something like 100k for R1) which will probably be higher than 600 \$\Omega\$.  

For line level connections, old equipment was often matched 600 \$\Omega\$ in/out. Nowadays however it's usually Lo-Z out to Hi-Z in. The Hi-Z input is often 10 k\$\Omega\$, but can be higher. You could measure the resistance across your Mini KAOSS input (be sure to do it after any DC blocking cap if present) to find out exactly what you are working with. YOu could also measure your pickups DC resistance to get a rough idea there too.  

I can only see a line in connection, which will probably be expecting a lower impedance signal than your guitar can provide. Have you tried putting your guitar through a preamplifier/DI box?

There may possibly be a DC blocking input cap you may have removed, which might cause strange things to happen.  

Here is a clip of a typical guitar amp input to give you an idea of what it expects to see. Note the 1 M\$\Omega\$ input resistor.
I'm no expert on guitar (passive coil) pickups but I think they are commonly around 5-20k (varies with frequency)
A piezo pickup will be much much higher.