Looking around online I found several schematics that were close to what I wanted but no cigar. The hub needed to plug onto an internal USB header with optional power to it, with a pass through of the unused port of the header. The hub needed to have pins rather than sockets to suit accessories intended for internal connection.
I messed up the mk1 pcb by missing 3 components, these were bodge wired on to get it working, the other issue was that it obstructed the 2nd motherboard USB header requiring a move.
The hub chips do not monitor the actual current as when powered it is external to them so I included PPTC fuses on the power outputs, equally when unpowered 100uf caps are there just in case :)
I am uploading just the schematic as that is working, ( the mk2 pcb's are in the post )
The PWR suffix on the schematic is used in the design rules for auto routing with a track width of 1mm, non PWR tracks are .3mm wide, PWR and non PWR are linked on the pcb with 1206 zero ohm links that are not shown on the schematic.