1.GLM import ---> Yes you get rid of the tags (personnaly, that's what i'd do!)
2.The bonecap file doesnt do anything as far as i know, just ignore it.
3.There is no way to quickly recompile a model if you dont have the ORIGINAL max file.
4.You wont see any tail bone errors, the reason is simple: in reality, you dont have to add every bone to the mesh for the GLA/GLM to work correctly. Of course there are exceptions...like i said, stick to the JO method and simply alter the skeleton when you want a "JA only" player model.
Here's a link of the bones you need to remove from the skin modifier stack (or simply delete them from the skeleton).
http://www3.sympatico.ca/psykopat/tutorials/carcassnew.jpg)
The reason you have to get rid of those bones, is that the .GLA file doesnt know what to do with these extra bones (there are no animations for them...so theyre not needed anymore)