Here is a picture of the scratch on my 03 Subaru WRX:



For a scratch that size which would be a more effective solution, a Paint Bottle Kit or Spray Can Kit?  In addition, the bare metal has just started to rust.  Would purchasing Rust Converter be overkill?  Should I just sand through the rust?  I would greatly appreciate any other work approach or product recommendations as well.

From your picture, it looks like surface rust which you can sand off. If it has started to pit at all, you should use a rust converter on it but i don't think it is this bad.

I would sand the rust off, prime the area and use the paint pen to repair this area.