For JA shaders go in base\shaders as you said; shaderlist.txt is still used, if you don't specify a shader file in shaderlist.txt q3map2 will NOT use it for compiling - but JA will still read the shader of course.
JA shaders don't use .tga, .jpg or any other extensions in the files; that's quite important.
Besides that I see no real problems, just get GTKRadiant 1.4 from
www.qeradiant.com) and it'll come set up to use Q3Map2.