Those are the old-style connectors. Use your chassis number in RealOEM, it'll probably have the new style connectors, same as what is fitted now (tip: look at your own car to see the connectors in real life)

As for coax cabling, I wouldn't destroy the wiring if it was my car.
If you do a neat and tidy job with the coax, it won't affect reception. But I wouldn't do it to my car....

As for the GPS antenna, you need an adapter. You have no choice.

SMBs can be found in every country, go and contact your local specialised coax cable manufacturer. SMBs are used in the mobile telephone industry for base stations, you won't find them in a hobby shop, but you will find them at a cable manufacturer.

And Mk4 navs are the same world-wide, so no problem there. Make sure you program it afterwards to suit your car (NavCoder can do this for you)