I'm still a bit confused by your description, photos' would really help.
But, if I understand the original problem of the underfloor mount having the trans cross member in the way of the master cylinder......would it be possible to mount the master further back, behind the cross member and simply install a longer rod between the pedal mount and the master. This long rod could run through a hole in the cross member. As I said, pics would really help!!!
This photo shows a link rod. It could be as long as needed, as long as its' diameter is big enough to keep it from flexing under load.
Hope this makes sense and helps a bit.