I use V4.x and have 7 switches actually. Assuming you are going to use the switches in NC (Normally Closed) configuration, put the switches for each axis in series. Then when 4.01 comes out, you will be set for the home switch option. If you are planning on NO (Normally Open), put the switches in parallel.
As for the override, what I do is press the F8 key and in continious mode, back off the axis that is causing the problem. Be sure to toggle the limit switches OFF to be able to do this!
I agree with you, as I also miss the message that tells me WHICH axis is at fault, but it is not to much of a pain to simply look at the various axis and it is easy to tell which one has tripped. No need for a seperate override! Of course this is with my setup and breakout board, so YMMV