Could anyone let me know whether I should keep or remove the kidney box when fitting an aftermarket breather, such as a bailey etc.

What are the advantages of keeping or removing it?

 

if you keep it - it would be like fitting a big bore tailpipe to a std bore system = just for looks. it causes a restriction in the bretaher system, if you are fitting an uprated breather system, why leave the original one inplace? as that is all the box is - an oil seperator - NOT a flame trap even though some people continue to call it that.